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. By contrast,
+our General Public Licenses are intended to guarantee your freedom to
+share and change all versions of a program--to make sure it remains free
+software for all its users.
+
+ When we speak of free software, we are referring to freedom, not
+price. Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+them if you wish), that you receive source code or can get it if you
+want it, that you can change the software or use pieces of it in new
+free programs, and that you know you can do these things.
+
+ Developers that use our General Public Licenses protect your rights
+with two steps: (1) assert copyright on the software, and (2) offer
+you this License which gives you legal permission to copy, distribute
+and/or modify the software.
+
+ A secondary benefit of defending all users' freedom is that
+improvements made in alternate versions of the program, if they
+receive widespread use, become available for other developers to
+incorporate. Many developers of free software are heartened and
+encouraged by the resulting cooperation. However, in the case of
+software used on network servers, this result may fail to come about.
+The GNU General Public License permits making a modified version and
+letting the public access it on a server without ever releasing its
+source code to the public.
+
+ The GNU Affero General Public License is designed specifically to
+ensure that, in such cases, the modified source code becomes available
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+users of that server. Therefore, public use of a modified version, on
+a publicly accessible server, gives the public access to the source
+code of the modified version.
+
+ An older license, called the Affero General Public License and
+published by Affero, was designed to accomplish similar goals. This is
+a different license, not a version of the Affero GPL, but Affero has
+released a new version of the Affero GPL which permits relicensing under
+this license.
+
+ The precise terms and conditions for copying, distribution and
+modification follow.
+
+ TERMS AND CONDITIONS
+
+ 0. Definitions.
+
+ "This License" refers to version 3 of the GNU Affero General Public License.
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+ "Copyright" also means copyright-like laws that apply to other kinds of
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+ "The Program" refers to any copyrightable work licensed under this
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+ To "modify" a work means to copy from or adapt all or part of the work
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+
+ A patent license is "discriminatory" if it does not include within
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+the work, and under which the third party grants, to any of the
+parties who would receive the covered work from you, a discriminatory
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+or that patent license was granted, prior to 28 March 2007.
+
+ Nothing in this License shall be construed as excluding or limiting
+any implied license or other defenses to infringement that may
+otherwise be available to you under applicable patent law.
+
+ 12. No Surrender of Others' Freedom.
+
+ If conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
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+covered work so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you may
+not convey it at all. For example, if you agree to terms that obligate you
+to collect a royalty for further conveying from those to whom you convey
+the Program, the only way you could satisfy both those terms and this
+License would be to refrain entirely from conveying the Program.
+
+ 13. Remote Network Interaction; Use with the GNU General Public License.
+
+ Notwithstanding any other provision of this License, if you modify the
+Program, your modified version must prominently offer all users
+interacting with it remotely through a computer network (if your version
+supports such interaction) an opportunity to receive the Corresponding
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+means of facilitating copying of software. This Corresponding Source
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+of the GNU General Public License that is incorporated pursuant to the
+following paragraph.
+
+ Notwithstanding any other provision of this License, you have
+permission to link or combine any covered work with a work licensed
+under version 3 of the GNU General Public License into a single
+combined work, and to convey the resulting work. The terms of this
+License will continue to apply to the part which is the covered work,
+but the work with which it is combined will remain governed by version
+3 of the GNU General Public License.
+
+ 14. Revised Versions of this License.
+
+ The Free Software Foundation may publish revised and/or new versions of
+the GNU Affero General Public License from time to time. Such new versions
+will be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+ Each version is given a distinguishing version number. If the
+Program specifies that a certain numbered version of the GNU Affero General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation. If the Program does not specify a version number of the
+GNU Affero General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+ If the Program specifies that a proxy can decide which future
+versions of the GNU Affero General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+ Later license versions may give you additional or different
+permissions. However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+ 15. Disclaimer of Warranty.
+
+ THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+ 16. Limitation of Liability.
+
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+
+ Copyright (C)
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Affero General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU Affero General Public License for more details.
+
+ You should have received a copy of the GNU Affero General Public License
+ along with this program. 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)
+ )
+})