diff --git a/DESCRIPTION b/DESCRIPTION index 77cf88f..ddeedd3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -33,7 +33,9 @@ Imports: assertthat, dplyr, future.apply, - phyloregion, + Matrix, + methods, + phangorn, progressr, purrr, stats, @@ -51,7 +53,8 @@ Suggests: stringr, magrittr, covr, - picante + picante, + phyloregion Config/testthat/edition: 3 Depends: R (>= 3.5.0) diff --git a/R/calc_biodiv_random.R b/R/calc_biodiv_random.R index f567121..b30fc95 100644 --- a/R/calc_biodiv_random.R +++ b/R/calc_biodiv_random.R @@ -115,12 +115,12 @@ calc_biodiv_random <- function(comm, phy, phy_alt, # Calculations ---- - # Convert comm to sparse matrix format for phyloregions - comm_sparse <- phyloregion::dense2sparse(comm) + # Convert comm to sparse matrix format + comm_sparse <- dense2sparse(comm) # Generate random community random_comm <- cpr_rand_comm(comm, null_model = null_model, n_iterations = n_iterations, thin = thin, seed = seed) - random_comm_sparse <- phyloregion::dense2sparse(random_comm) + random_comm_sparse <- dense2sparse(random_comm) # Calculate statistics for random community # - set up null vectors first @@ -132,20 +132,20 @@ calc_biodiv_random <- function(comm, phy, phy_alt, rpe <- NULL # - calculate selected metrics - if ("pd" %in% metrics) pd <- phyloregion::PD(random_comm_sparse, phy) - if ("pd_alt" %in% metrics) pd_alt <- phyloregion::PD(random_comm_sparse, phy_alt) + if ("pd" %in% metrics) pd <- PD(random_comm_sparse, phy) + if ("pd_alt" %in% metrics) pd_alt <- PD(random_comm_sparse, phy_alt) # pd_alt is inferred by rpd if ("rpd" %in% metrics) { - if (is.null(pd)) pd <- phyloregion::PD(random_comm_sparse, phy) - if (is.null(pd_alt)) pd_alt <- phyloregion::PD(random_comm_sparse, phy_alt) + if (is.null(pd)) pd <- PD(random_comm_sparse, phy) + if (is.null(pd_alt)) pd_alt <- PD(random_comm_sparse, phy_alt) rpd <- pd / pd_alt } # pe_alt is inferred by rpe - if ("pe" %in% metrics) pe <- phyloregion::phylo_endemism(random_comm_sparse, phy, weighted = TRUE) - if ("pe_alt" %in% metrics) pe_alt <- phyloregion::phylo_endemism(random_comm_sparse, phy_alt, weighted = TRUE) + if ("pe" %in% metrics) pe <- phylo_endemism(random_comm_sparse, phy, weighted = TRUE) + if ("pe_alt" %in% metrics) pe_alt <- phylo_endemism(random_comm_sparse, phy_alt, weighted = TRUE) if ("rpe" %in% metrics) { - if (is.null(pe)) pe <- phyloregion::phylo_endemism(random_comm_sparse, phy, weighted = TRUE) - if (is.null(pe_alt)) pe_alt <- phyloregion::phylo_endemism(random_comm_sparse, phy_alt, weighted = TRUE) + if (is.null(pe)) pe <- phylo_endemism(random_comm_sparse, phy, weighted = TRUE) + if (is.null(pe_alt)) pe_alt <- phylo_endemism(random_comm_sparse, phy_alt, weighted = TRUE) rpe <- pe / pe_alt } diff --git a/R/cpr_rand_test.R b/R/cpr_rand_test.R index e8d97c5..361046d 100644 --- a/R/cpr_rand_test.R +++ b/R/cpr_rand_test.R @@ -151,8 +151,8 @@ cpr_rand_test <- function(comm, phy, null_model, #' convert to integer before numeric comparisons # - null_model assertthat::assert_that( - assertthat::is.string(null_model) | inherits(null_model, "commsim"), - msg = "'null_model' must be a string (character vector of length 1) or an object of class 'commsim'" + assertthat::is.string(null_model) | inherits(null_model, "commsim"), + msg = "'null_model' must be a string (character vector of length 1) or an object of class 'commsim'" ) assertthat::assert_that(assertthat::noNA(null_model)) # - n_reps @@ -229,7 +229,7 @@ cpr_rand_test <- function(comm, phy, null_model, comm <- comm_df } #' @srrstats {UL1.2} Check for default-looking rownames - # Default rownames not allowed because phyloregion::dense2sparse() will convert them to NULL + # Default rownames not allowed because dense2sparse() will convert them to NULL assertthat::assert_that( !identical(rownames(comm), as.character(seq(nrow(comm)))), msg = "'comm' cannot have default row names (consecutive integers from 1 to the number of rows)" @@ -364,7 +364,7 @@ cpr_rand_test <- function(comm, phy, null_model, phy$edge.length <- phy$edge.length / sum(phy$edge.length) # Make sparse community df - comm_sparse <- phyloregion::dense2sparse(comm) + comm_sparse <- dense2sparse(comm) # Calculate biodiversity metrics ---- @@ -398,26 +398,26 @@ cpr_rand_test <- function(comm, phy, null_model, # - calculate selected metrics if ("pd" %in% metrics) { - pd_obs <- phyloregion::PD(comm_sparse, phy) + pd_obs <- PD(comm_sparse, phy) ses_pd <- get_ses(random_vals, pd_obs, "pd") } if ("rpd" %in% metrics) { - if (!exists("pd_obs")) pd_obs <- phyloregion::PD(comm_sparse, phy) - pd_alt_obs <- phyloregion::PD(comm_sparse, phy_alt) + if (!exists("pd_obs")) pd_obs <- PD(comm_sparse, phy) + pd_alt_obs <- PD(comm_sparse, phy_alt) ses_pd_alt <- get_ses(random_vals, pd_alt_obs, "pd_alt") rpd_obs <- pd_obs / pd_alt_obs ses_rpd <- get_ses(random_vals, rpd_obs, "rpd") } if ("pe" %in% metrics) { - pe_obs <- phyloregion::phylo_endemism(comm_sparse, phy, weighted = TRUE) + pe_obs <- phylo_endemism(comm_sparse, phy, weighted = TRUE) ses_pe <- get_ses(random_vals, pe_obs, "pe") } if ("rpe" %in% metrics) { - if (!exists("pe_obs")) pe_obs <- phyloregion::phylo_endemism(comm_sparse, phy, weighted = TRUE) - pe_alt_obs <- phyloregion::phylo_endemism(comm_sparse, phy_alt, weighted = TRUE) + if (!exists("pe_obs")) pe_obs <- phylo_endemism(comm_sparse, phy, weighted = TRUE) + pe_alt_obs <- phylo_endemism(comm_sparse, phy_alt, weighted = TRUE) ses_pe_alt <- get_ses(random_vals, pe_alt_obs, "pe_alt") rpe_obs <- pe_obs / pe_alt_obs ses_rpe <- get_ses(random_vals, rpe_obs, "rpe") diff --git a/R/get_ses.R b/R/get_ses.R index 5a6d4b0..06b74df 100644 --- a/R/get_ses.R +++ b/R/get_ses.R @@ -28,8 +28,8 @@ #' 1:100, #' ~ calc_biodiv_random(comm, phy, phy_alt, "independentswap", 1000L, metrics = "pe") #' ) -#' comm_sparse <- phyloregion::dense2sparse(comm) -#' pe_obs <- phyloregion::phylo_endemism(comm_sparse, phy, weighted = TRUE) +#' comm_sparse <- dense2sparse(comm) +#' pe_obs <- phylo_endemism(comm_sparse, phy, weighted = TRUE) #' get_ses(random_vals, pe_obs, "pe") #' } #' @autoglobal diff --git a/R/utils.R b/R/utils.R index 83f5521..4b01411 100644 --- a/R/utils.R +++ b/R/utils.R @@ -247,3 +247,61 @@ match_phylo_comm <- function(phy, comm) { res$comm <- comm[, res$phy$tip.label] return(res) } + +# Functions copied from phyloregion v1.0.6 under AGPL-3 ---- + +# Corresponds to phyloregion::dense2sparse() +dense2sparse <- function(x) { + x <- as.matrix(x) + Matrix::Matrix(x, sparse = TRUE) +} + +# Corresponds to phyloregion:::phylo_community() +phylo_community <- function(x, phy) { + el <- numeric(max(phy$edge)) + el[phy$edge[, 2]] <- phy$edge.length + x <- x[, phy$tip.label] + anc <- phangorn::Ancestors(phy, seq_along(phy$tip.label)) + anc <- mapply(c, seq_along(phy$tip.label), anc, SIMPLIFY = FALSE) + M <- Matrix::sparseMatrix(as.integer(rep( + seq_along(anc), + lengths(anc) + )), as.integer(unlist(anc)), x = 1L) + commphylo <- x %*% M + commphylo@x[commphylo@x > 1e-08] <- 1 + list(Matrix = commphylo, edge.length = el) +} + +# Corresponds to phyloregion::PD() +PD <- function(x, phy) { + if (!methods::is(x, "sparseMatrix")) { + stop("x needs to be a sparse matrix!") + } + if (length(setdiff(colnames(x), phy$tip.label)) > 0) { + stop("There are species labels in community matrix missing in the tree!") + } + if (length(setdiff(phy$tip.label, colnames(x))) > 0) { + phy <- ape::keep.tip(phy, intersect(phy$tip.label, colnames(x))) + } + x <- x[, intersect(phy$tip.label, colnames(x))] + z <- phylo_community(x, phy) + (z$Matrix %*% z$edge.length)[, 1] +} + +# Corresponds to phyloregion::phylo_endemism() +phylo_endemism <- function(x, phy, weighted = TRUE) { + if (length(setdiff(colnames(x), phy$tip.label)) > 0) { + stop("There are species labels in community matrix missing in the tree!") + } + if (length(setdiff(phy$tip.label, colnames(x))) > 0) { + phy <- ape::keep.tip(phy, intersect(phy$tip.label, colnames(x))) + } + comm_phylo <- phylo_community(x, phy) + weights <- comm_phylo$Matrix %*% Matrix::Diagonal(x = 1 / Matrix::colSums(comm_phylo$Matrix)) + if (weighted == FALSE) { + weights[weights < 1] <- 0 + } + pd <- (weights %*% comm_phylo$edge.length)[, 1] + pd <- pd[row.names(x)] + return(pd) +} diff --git a/README.Rmd b/README.Rmd index c5891a3..5cb31e3 100644 --- a/README.Rmd +++ b/README.Rmd @@ -53,7 +53,7 @@ library(canaper) data(phylocom) -# Example community matrix including 4 "clumped" communities, +# Example community matrix including 4 "clumped" communities, # one "even" community, and one "random" community phylocom$comm @@ -71,7 +71,7 @@ rand_test_results <- cpr_rand_test(phylocom$comm, phylocom$phy, null_model = "sw `cpr_rand_test` produces **a lot** of columns (nine per metric), so let's just look at a subset of them: ```{r rand-test-res} -rand_test_results[,1:9] +rand_test_results[, 1:9] ``` This is a summary of the columns: @@ -133,9 +133,10 @@ You can find DOIs for older versions by viewing the "Releases" menu on the right ## Licenses -- Code: [MIT](LICENSE.md) +- Original code: [MIT](LICENSE.md) +- Functions from [phyloregion](https://github.com/darunabas/phyloregion): [AGPL-3](https://github.com/joelnitta/canaper/blob/main/data-raw/LICENSE-agpl-3.txt) - Example datasets - - `acacia`, `biod_example`: [GNU General Public License v3.0](https://github.com/joelnitta/canaper/blob/main/data-raw/LICENSE-gpl.txt) + - `acacia`, `biod_example`: [GPL-3](https://github.com/joelnitta/canaper/blob/main/data-raw/LICENSE-gpl-3.txt) - `phylocom`: [BSD-3-Clause](https://github.com/joelnitta/canaper/blob/main/data-raw/LICENSE-bsd3.txt) ## References diff --git a/README.md b/README.md index e8e2ff3..bedc63a 100644 --- a/README.md +++ b/README.md @@ -49,7 +49,7 @@ library(canaper) data(phylocom) -# Example community matrix including 4 "clumped" communities, +# Example community matrix including 4 "clumped" communities, # one "even" community, and one "random" community phylocom$comm #> sp1 sp10 sp11 sp12 sp13 sp14 sp15 sp17 sp18 sp19 sp2 sp20 sp21 sp22 @@ -91,29 +91,29 @@ value to the alternative value (relative PD, relative PE). ``` r set.seed(071421) rand_test_results <- cpr_rand_test(phylocom$comm, phylocom$phy, null_model = "swap") -#> [1] "Dropping tips from the tree because they are not present in the community data:" -#> [1] "sp16" "sp23" "sp27" "sp28" "sp30" "sp31" "sp32" +#> Warning in match_phylo_comm(phy = phy, comm = comm): Dropping tips from the tree because they are not present in the community data: +#> sp16, sp23, sp27, sp28, sp30, sp31, sp32 ``` `cpr_rand_test` produces **a lot** of columns (nine per metric), so let’s just look at a subset of them: ``` r -rand_test_results[,1:9] +rand_test_results[, 1:9] #> pd_obs pd_rand_mean pd_rand_sd pd_obs_z pd_obs_c_upper -#> clump1 0.3018868 0.4692453 0.03214267 -5.206739 0 -#> clump2a 0.3207547 0.4762264 0.03263836 -4.763465 0 -#> clump2b 0.3396226 0.4681132 0.03462444 -3.710978 0 -#> clump4 0.4150943 0.4667925 0.03180131 -1.625660 3 -#> even 0.5660377 0.4660377 0.03501739 2.855724 100 -#> random 0.5094340 0.4733962 0.03070539 1.173662 79 +#> clump1 0.3018868 0.4675472 0.03623666 -4.571624 0 +#> clump2a 0.3207547 0.4684906 0.03116570 -4.740335 0 +#> clump2b 0.3396226 0.4684906 0.03150994 -4.089754 0 +#> clump4 0.4150943 0.4664151 0.03307178 -1.551799 3 +#> even 0.5660377 0.4641509 0.03517108 2.896891 100 +#> random 0.5094340 0.4713208 0.03295196 1.156629 80 #> pd_obs_c_lower pd_obs_q pd_obs_p_upper pd_obs_p_lower #> clump1 100 100 0.00 1.00 #> clump2a 100 100 0.00 1.00 #> clump2b 100 100 0.00 1.00 -#> clump4 91 100 0.03 0.91 +#> clump4 90 100 0.03 0.90 #> even 0 100 1.00 0.00 -#> random 6 100 0.79 0.06 +#> random 7 100 0.80 0.07 ``` This is a summary of the columns: @@ -145,7 +145,7 @@ canape_results[, "endem_type", drop = FALSE] #> clump2a not significant #> clump2b not significant #> clump4 not significant -#> even mixed +#> even super #> random mixed ``` @@ -192,10 +192,13 @@ the right. ## Licenses -- Code: [MIT](LICENSE.md) +- Original code: [MIT](LICENSE.md) +- Functions from + [phyloregion](https://github.com/darunabas/phyloregion): + [AGPL-3](https://github.com/joelnitta/canaper/blob/main/data-raw/LICENSE-agpl-3.txt) - Example datasets - - `acacia`, `biod_example`: [GNU General Public License - v3.0](https://github.com/joelnitta/canaper/blob/main/data-raw/LICENSE-gpl.txt) + - `acacia`, `biod_example`: + [GPL-3](https://github.com/joelnitta/canaper/blob/main/data-raw/LICENSE-gpl-3.txt) - `phylocom`: [BSD-3-Clause](https://github.com/joelnitta/canaper/blob/main/data-raw/LICENSE-bsd3.txt) diff --git a/codemeta.json b/codemeta.json index c0e6237..0066251 100644 --- a/codemeta.json +++ b/codemeta.json @@ -205,6 +205,18 @@ "url": "https://cran.r-project.org" }, "sameAs": "https://CRAN.R-project.org/package=picante" + }, + { + "@type": "SoftwareApplication", + "identifier": "phyloregion", + "name": "phyloregion", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, + "sameAs": "https://CRAN.R-project.org/package=phyloregion" } ], "softwareRequirements": [ @@ -270,15 +282,32 @@ }, { "@type": "SoftwareApplication", - "identifier": "phyloregion", - "name": "phyloregion", + "identifier": "Matrix", + "name": "Matrix", "provider": { "@id": "https://cran.r-project.org", "@type": "Organization", "name": "Comprehensive R Archive Network (CRAN)", "url": "https://cran.r-project.org" }, - "sameAs": "https://CRAN.R-project.org/package=phyloregion" + "sameAs": "https://CRAN.R-project.org/package=Matrix" + }, + { + "@type": "SoftwareApplication", + "identifier": "methods", + "name": "methods" + }, + { + "@type": "SoftwareApplication", + "identifier": "phangorn", + "name": "phangorn", + "provider": { + "@id": "https://cran.r-project.org", + "@type": "Organization", + "name": "Comprehensive R Archive Network (CRAN)", + "url": "https://cran.r-project.org" + }, + "sameAs": "https://CRAN.R-project.org/package=phangorn" }, { "@type": "SoftwareApplication", @@ -341,7 +370,7 @@ } ], "releaseNotes": "https://github.com/joelnitta/canaper/blob/master/NEWS.md", - "fileSize": "7891.09KB", + "fileSize": "7891.857KB", "contIntegration": ["https://github.com/joelnitta/canaper/actions", "https://codecov.io/gh/joelnitta/canaper?branch=main"], "developmentStatus": "https://www.repostatus.org/#wip", "keywords": [ diff --git a/data-raw/LICENSE-agpl-3.txt b/data-raw/LICENSE-agpl-3.txt new file mode 100644 index 0000000..be3f7b2 --- /dev/null +++ b/data-raw/LICENSE-agpl-3.txt @@ -0,0 +1,661 @@ + GNU AFFERO GENERAL PUBLIC LICENSE + Version 3, 19 November 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU Affero General Public License is a free, copyleft license for +software and other kinds of works, specifically designed to ensure +cooperation with the community in the case of network server software. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If your software can interact with users remotely through a computer +network, you should also make sure that it provides a way for users to +get its source. For example, if your program is a web application, its +interface could display a "Source" link that leads users to an archive +of the code. There are many ways you could offer source, and different +solutions will be better for different programs; see section 13 for the +specific requirements. + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU AGPL, see +. diff --git a/inst/WORDLIST b/inst/WORDLIST index b3da5d1..9fe1e8a 100644 --- a/inst/WORDLIST +++ b/inst/WORDLIST @@ -1,13 +1,112 @@ Affero -MERCHANTABILITY -Sublicensing -WIPO +AGPL +al +anthonynorth +assertr +assertthat +aut +Biodiverse +bioRxiv +BugReports +canaper +CMD +codecov +Codecov +codemeta +codeRepository +Commun +ComputerLanguage +Config +contIntegration copyrightable +copyrightHolder +covr +cran +cre +ctb +datePublished +developmentStatus +doi +DOI +DOIs +dplyr +dtc +endemism +Endemism +et +familyName +fileSize fsf +funder +gh +github +givenName +gmail +González +http https +io +issueTracker +Iwasaki +joelnitta +Knerr +knitr +Laffan +LazyData lgpl licensors +magrittr +md +MERCHANTABILITY +Mishler +ncomms +neo +neoendemic +Nitta noncommercially +orcid +ORCID +Orozco +paleo +Paleo +paleoendemic +phangorn +Phylocom +phyloregion +programmingLanguage +progressr +purrr +readme +README +releaseNotes relicensing +renv +repostatus +rmarkdown +roclet +roclets +Roxygen +RoxygenNote +roxyglobals +runtimePlatform +sameAs +SoftwareApplication +softwareRequirements +SoftwareSourceCode +softwareSuggestions +spdx +srr +stringr sublicenses +Sublicensing +testthat +tibble +tictoc +tidyverse +VignetteBuilder +Wataru +wip +WIP +WIPO www +zenodo diff --git a/tests/testthat/test-calc_biodiv_random.R b/tests/testthat/test-calc_biodiv_random.R index 8eec22b..5852c9d 100644 --- a/tests/testthat/test-calc_biodiv_random.R +++ b/tests/testthat/test-calc_biodiv_random.R @@ -58,53 +58,6 @@ test_that("Random seeds work", { expect_true(isTRUE(all.equal(res2, res4))) }) -test_that("Random seeds work in parallel", { - skip("WIP: need to figure out how to use future.apply reproducibly in a package") - # If run without sourcing files in R/, get error: - # Error in calc_biodiv_random(comm, phy, phy_alt, "curveball", 100L) : - # could not find function "calc_biodiv_random" - - # Change back to sequential when done (including on failure) - on.exit(future::plan(future::sequential), add = TRUE) - - # Set future resolution to parallelized, with 3 workers - future::plan(future::multisession, workers = 3) - - set.seed(12345) - res1 <- future.apply::future_lapply( - 1:2, - function(x) { - calc_biodiv_random(comm, phy, phy_alt, "curveball", 100L) - }, - future.seed = TRUE - ) - set.seed(67890) - res2 <- future.apply::future_lapply( - 1:2, - function(x) { - calc_biodiv_random(comm, phy, phy_alt, "curveball", 100L) - }, - future.seed = TRUE - ) - # Should be able to pass seed as an argument - set.seed(12345) - res3 <- future.apply::future_lapply( - 1:2, - function(x) { - calc_biodiv_random(comm, phy, phy_alt, "curveball", 100L) - }, - future.seed = TRUE - ) - # Different seeds should give different results - expect_false(isTRUE(all.equal(res1, res2))) - # Same seeds should give same results - expect_true(isTRUE(all.equal(res1, res3))) - - # Change back to sequential - future::plan(future::sequential) -}) - - test_that("Output is formatted as expected", { #' @srrstats {G5.3} check that output has no missing values expect_true( diff --git a/tests/testthat/test-cpr_rand_test.R b/tests/testthat/test-cpr_rand_test.R index ed33f03..e64ee16 100644 --- a/tests/testthat/test-cpr_rand_test.R +++ b/tests/testthat/test-cpr_rand_test.R @@ -327,10 +327,6 @@ test_that("Seeds work across sequential and parallel", { # Set future resolution to parallelized, with 3 workers future::plan(future::multisession, workers = 3) - # FIXME: for some bizarre reason, need to "prime" seed with a single run first. - # need to come up with a better solution - par_res_0 <- cpr_rand_test(phylocom$comm, phylocom$phy, null_model = "curveball", n_iterations = 10, n_reps = 10, quiet = TRUE) - # then the rest of the set.seed() calls work set.seed(12345) par_res_1 <- cpr_rand_test(biod_example$comm, biod_example$phy, null_model = "curveball", n_iterations = 10, n_reps = 10) set.seed(67890) @@ -448,18 +444,18 @@ test_that("Various randomization algorithms work", { }) test_that("Custom randomization algorithms work", { - randomizer <- function(x, n, ...) { - array(replicate(n, sample(x)), c(dim(x), n)) - } - cs_object <- vegan::commsim( - "r00_model", - fun = randomizer, binary = TRUE, - isSeq = FALSE, mode = "integer" - ) - set.seed(12345) - expect_snapshot( - cpr_rand_test(phylocom$comm, phylocom$phy, cs_object, n_reps = 10, quiet = TRUE) - ) + randomizer <- function(x, n, ...) { + array(replicate(n, sample(x)), c(dim(x), n)) + } + cs_object <- vegan::commsim( + "r00_model", + fun = randomizer, binary = TRUE, + isSeq = FALSE, mode = "integer" + ) + set.seed(12345) + expect_snapshot( + cpr_rand_test(phylocom$comm, phylocom$phy, cs_object, n_reps = 10, quiet = TRUE) + ) }) # Cleanup ---- diff --git a/tests/testthat/test-get_ses.R b/tests/testthat/test-get_ses.R index 2e5ff4a..39b9d69 100644 --- a/tests/testthat/test-get_ses.R +++ b/tests/testthat/test-get_ses.R @@ -11,8 +11,8 @@ random_vals <- 1:100, ~ calc_biodiv_random(comm, phy, phy_alt, "curveball", 1000L, metrics = "pe") ) -comm_sparse <- phyloregion::dense2sparse(comm) -pe_obs <- phyloregion::phylo_endemism(comm_sparse, phy, weighted = TRUE) +comm_sparse <- dense2sparse(comm) +pe_obs <- phylo_endemism(comm_sparse, phy, weighted = TRUE) # Run tests ---- diff --git a/tests/testthat/test-utils.R b/tests/testthat/test-utils.R index 34524d5..666e595 100644 --- a/tests/testthat/test-utils.R +++ b/tests/testthat/test-utils.R @@ -83,10 +83,10 @@ test_that("Printing phylogenies works", { test_that("Matching community and phylogeny data works", { comm_small <- biod_example$comm[, !colnames(biod_example$comm) %in% c("sp3", "sp5")] phy_small <- ape::drop.tip(biod_example$phy, c("sp1", "sp2")) - dat_small_1 <- match_phylo_comm(biod_example$phy, comm_small) - dat_small_2 <- match_phylo_comm(phy_small, biod_example$comm) - dat_small_3 <- match_phylo_comm(phy_small, comm_small) - dat_matched <- match_phylo_comm(biod_example$phy, biod_example$comm) + dat_small_1 <- suppressWarnings(match_phylo_comm(biod_example$phy, comm_small)) + dat_small_2 <- suppressWarnings(match_phylo_comm(phy_small, biod_example$comm)) + dat_small_3 <- suppressWarnings(match_phylo_comm(phy_small, comm_small)) + dat_matched <- suppressWarnings(match_phylo_comm(biod_example$phy, biod_example$comm)) dat_small_1_pic <- picante::match.phylo.comm(biod_example$phy, comm_small) dat_small_2_pic <- picante::match.phylo.comm(phy_small, biod_example$comm) dat_small_3_pic <- picante::match.phylo.comm(phy_small, comm_small) @@ -108,12 +108,12 @@ test_that("Matching community and phylogeny data works", { ) # Make sure order of community species doesn't matter for PD, PE expect_equal( - phyloregion::PD(phyloregion::dense2sparse(dat_matched$comm), dat_matched$phy), - phyloregion::PD(phyloregion::dense2sparse(biod_example$comm), biod_example$phy) + PD(dense2sparse(dat_matched$comm), dat_matched$phy), + PD(dense2sparse(biod_example$comm), biod_example$phy) ) expect_equal( - phyloregion::phylo_endemism(phyloregion::dense2sparse(dat_matched$comm), dat_matched$phy), - phyloregion::phylo_endemism(phyloregion::dense2sparse(biod_example$comm), biod_example$phy) + phylo_endemism(dense2sparse(dat_matched$comm), dat_matched$phy), + phylo_endemism(dense2sparse(biod_example$comm), biod_example$phy) ) # Warnings work expect_warning( @@ -138,3 +138,27 @@ test_that("Matching community and phylogeny data works", { fixed = TRUE ) }) + +test_that("Functions copied from phyloregion work", { + expect_equal( + dense2sparse(biod_example$comm), + phyloregion::dense2sparse(biod_example$comm) + ) + sparse_comm <- dense2sparse(biod_example$comm) + expect_equal( + phylo_community(sparse_comm, biod_example$phy), + phyloregion:::phylo_community(dense2sparse(biod_example$comm), biod_example$phy) + ) + expect_equal( + PD(sparse_comm, biod_example$phy), + phyloregion::PD(sparse_comm, biod_example$phy) + ) + expect_equal( + phylo_endemism(sparse_comm, biod_example$phy, weighted = TRUE), + phyloregion::phylo_endemism(sparse_comm, biod_example$phy, weighted = TRUE) + ) + expect_equal( + phylo_endemism(sparse_comm, biod_example$phy, weighted = FALSE), + phyloregion::phylo_endemism(sparse_comm, biod_example$phy, weighted = FALSE) + ) +})