context("Right output management") test_that("make.output.data.frame works", { ## Generating some data tree <- ape::read.tree(text = "((((((1,2),3),4),5),6),(7,(8,(9,(10,(11,12))))));") character <- "23--1??--032" NA_matrix <- apply.reconstruction(tree, character, passes = 4, method = "NA") Fitch_matrix <- apply.reconstruction(tree, character, passes = 2, method = "Fitch") ## Creating the output matrix test_NA <- make.output.data.frame(NA_matrix) test_Fitch <- make.output.data.frame(Fitch_matrix) ## Right output type expect_is(test_NA, "data.frame") expect_is(test_Fitch, "data.frame") expect_equal(dim(test_NA), c(23, 7)) expect_equal(dim(test_Fitch), c(23, 4)) ## Right output values expect_is(test_NA$Dp1, "character") expect_is(test_NA$Up1, "character") expect_is(test_NA$Dp2, "character") expect_is(test_NA$Up2, "character") expect_is(test_NA$Changes, "logical") expect_is(test_NA$Regions, "logical") expect_is(test_Fitch$Dp1, "character") expect_is(test_Fitch$Up1, "character") expect_is(test_Fitch$Dp2, "NULL") expect_is(test_Fitch$Up2, "NULL") expect_is(test_Fitch$Changes, "logical") expect_is(test_Fitch$Regions, "NULL") }) test_that("write.tree.commented works", { ## Generating some data tree <- ape::read.tree(text = "((((((1,2),3),4),5),6),(7,(8,(9,(10,(11,12))))));") character <- "23--1??--032" NA_matrix <- apply.reconstruction(tree, character, passes = 4, method = "NA") test_NA <- make.output.data.frame(NA_matrix) ## Create the notes node_notes <- lapply(as.list(1:(ape::Ntip(NA_matrix$tree) + ape::Nnode(NA_matrix$tree))), create.note, test_NA) expect_is(node_notes, "list") expect_equal(length(node_notes), 23) expect_is(unlist(unique(lapply(node_notes, class))), "character") expect_equal(node_notes[[1]], "[Dp1=2,Up1=2,Dp2=2,Up2=2,Changes=FALSE,Regions=TRUE]") expect_equal(node_notes[[10]], "[Dp1=0,Up1=0,Dp2=0,Up2=0,Changes=FALSE,Regions=TRUE]") expect_equal(node_notes[[23]], "[Dp1=23,Up1=23,Dp2=23,Up2=023,Changes=TRUE,Regions=TRUE]") ## Check writing the notes set.seed(1) tree <- ape::rtree(5, br = NULL) node_notes <- lapply(as.list(seq(1:9)), function(X){paste("[", X, "]", sep = "")}) newick <- write.tree.commented(tree, comments = node_notes, file = "") newick_decomp <- unlist(strsplit(strsplit(newick, split = ",")[[1]], split = ")")) expect_results <- unlist(node_notes)[c(1,2,7,3,4,5,9,8,6)] for(i in 1:length(newick_decomp)) { expect_equal(length(grep(expect_results[i], newick_decomp[i])), 1) } }) test_that("write.nexus.commented works", { ## Check writing the notes set.seed(1) tree <- ape::rtree(5, br = NULL) node_notes <- lapply(as.list(seq(1:9)), function(X){paste("[", X, "]", sep = "")}) out <- capture.output(write.nexus.commented(tree, comments = node_notes, file = "")) expect_equal(out[-2], c( "#NEXUS", "[More for at https://github.com/TGuillerme/Inapp/]", "", "BEGIN TAXA;", "\tDIMENSIONS NTAX = 5;", "\tTAXLABELS", "\t\tt3", "\t\tt4", "\t\tt1", "\t\tt2", "\t\tt5", "\t;", "END;", "BEGIN TREES;", "\tTRANSLATE", "\t\t1\tt3,", "\t\t2\tt4,", "\t\t3\tt1,", "\t\t4\tt2,", "\t\t5\tt5", "\t;", "\tTREE * UNTITLED = [&R] ((1[1],2[2])[7],(3[3],(4[4],5[5])[9])[8])[6];", "END;" )) }) test_that("read.key work", { expect_message(read.key("a", "b", scan = FALSE)) # expect_message(read.key("a", "b", scan = TRUE)) }) test_that("convert.binary.value work", { ## A random 5 taxa tree set.seed(1) tree <- ape::rtree(5, br = NULL) ## A character with inapplicable data character <- "01-?1" ## NA algorithm states_matrix <- apply.reconstruction(tree, character, passes = 4, method = "NA") expect_equal(unlist(convert.binary.value(states_matrix[[1]], states_matrix)), c(2, 4, 1, 7, 4, 0, 0, 0, 0)) ## Individual conversions work ## NA = 0 expect_equal(unlist(convert.binary.value(list(NULL), states_matrix)), 0) ## -1 = 1 expect_equal(unlist(convert.binary.value(list(-1), states_matrix)), 1) ## 0 = 2 expect_equal(unlist(convert.binary.value(list(0), states_matrix)), 2) ## c(-1,0) = 3 expect_equal(unlist(convert.binary.value(list(c(-1, 0)), states_matrix)), 3) ## 1 = 4 expect_equal(unlist(convert.binary.value(list(1), states_matrix)), 4) ## c(-1, 1) = 5 expect_equal(unlist(convert.binary.value(list(c(-1,1)), states_matrix)), 5) ## c(0, 1) = 6 expect_equal(unlist(convert.binary.value(list(c(0,1)), states_matrix)), 6) ## c(-1, 0, 1) = 7 expect_equal(unlist(convert.binary.value(list(c(-1,0,1)), states_matrix)), 7) }) test_that("get.missing work", { all_states <- c(1,2) expect_equal(get.missing(1, all_states), 1) expect_equal(get.missing(2, all_states), 2) expect_equal(get.missing(c(1,2), all_states), "?") }) test_that("output.results works properly", { ## A random 5 taxa tree set.seed(1) tree <- ape::rtree(5, br = NULL) ## A character with inapplicable data character <- "01-?1" ## NA algorithm NA_matrix <- apply.reconstruction(tree, character, passes = 4, method = "NA") ## Errors expect_error(output.states.matrix("NA_matrix", output = NULL, file = "Inapp_reconstruction", path = ".")) expect_error(output.states.matrix(NA_matrix, output = "NULL", file = "Inapp_reconstruction", path = ".")) expect_error(output.states.matrix(NA_matrix, output = 1, file = "Inapp_reconstruction", path = ".")) expect_error(output.states.matrix(NA_matrix, output = c("pdf", "csv"), file = "Inapp_reconstruction", path = ".")) expect_error(output.states.matrix(NA_matrix, output = "csv", file = c("a", "b"), path = ".")) expect_error(output.states.matrix(NA_matrix, output = "csv", file = "Inapp_reconstruction", path = c("a", "b"))) ## NULL return expect_null(output.states.matrix(NA_matrix, output = NULL, file = "Inapp_reconstruction", path = ".")) ## Exporting the results as an annotated newick tree expect_null(output.states.matrix(NA_matrix, output = "newick")) ## Exporting the results and notes in a nexus file expect_null(output.states.matrix(NA_matrix, output = "nexus")) ## Exporting the result in a csv expect_null(output.states.matrix(NA_matrix, output = "csv")) ## Exporting the plot as a pdf expect_null(output.states.matrix(NA_matrix, output = "pdf")) ## Exporting the plot as C-test expect_null(output.states.matrix(NA_matrix, output = "C-test")) })