version 0.2.0

DESCRIPTION

@@ -1,10 +1,10 @@
 Package: DarkDiv
 Type: Package
-Title: Estimating Probabilistic Dark Diversity
-Version: 0.1.0
+Title: Estimating Dark Diversity and Site-Specific Species Pools
+Version: 0.2.0
 Author: Carlos P. Carmona
 Maintainer: Carlos P. Carmona <perezcarmonacarlos@gmail.com>
-Description: Estimation of dark diversity using species co-occurrences. 
+Description: Estimation of dark diversity and site-specific species pools using species co-occurrences. 
     It includes implementations of probabilistic dark diversity based on the 
     Hypergeometric distribution, as well as estimations based on the Beals index,
     which can be transformed to binary predictions using different thresholds, 
@@ -22,6 +22,6 @@ RoxygenNote: 6.1.1
 Imports: vegan, stats
 Suggests: testthat
 NeedsCompilation: no
-Packaged: 2019-04-27 15:27:17 UTC; carlosperezcarmona
+Packaged: 2020-02-12 14:52:29 UTC; c.p.carmona
 Repository: CRAN
-Date/Publication: 2019-04-27 16:10:03 UTC
+Date/Publication: 2020-02-12 15:20:05 UTC

MD5

@@ -1,6 +1,6 @@
-a15b58fdd7f7dc1782cf3b8576fd06e6 *DESCRIPTION
+08c858ef5eef2949d6cdf60d11802305 *DESCRIPTION
 817d6a403e94463dd4df5afba9ebc71b *NAMESPACE
 045ed726fdced75a5c89be1dba9cfefe *R/DarkDiv.R
-d1e63cd5cf99f1fbef10a6342fbd53c0 *R/utility_functions.R
+d4bbed99767212586a534d0e94d708b2 *R/utility_functions.R
 74f12839f852716c0b3b28c10148c4d8 *man/DarkDiv.Rd
-70f2dc536da264419a13c1c3e28f2926 *tests/testthat.R
+446ee71fe36d37609acaf68961eced81 *tests/testthat/testthat.R

R/utility_functions.R

@@ -111,7 +111,7 @@ BealsThres <- function(Beals, limit = NULL, const = 0.01, r, x){
   ## thresholds for each specis
   q <- numeric(ncol(r))
   t <- Beals$t
-  b <- Beals$rawBealsPool
+  b <- Beals$Pool
   for (j in 1:ncol(r)){
     q[j] <- 1
     if (limit == "min" & sum(r[, j]) > 0){

tests/testthat.R → tests/testthat/testthat.R

@@ -1,39 +1,39 @@
-library(testthat)
-library(DarkDiv)
-
-test_that("Beals gives same results as vegan", {
-  require(vegan)
-  data(dune)
-  BealsDD <- DarkDiv(x = dune, method = "RawBeals")
-  BealsVegan <- vegan::beals(x = dune, type = 0, include=F)
-  expect_equal(BealsDD$AllProbs, BealsVegan)
-})
-
-test_that("Using indication matrix directly yields same results as reference", {
-  require(vegan)
-  data(dune)
-  #RawBeals
-  ddBeals <- DarkDiv(x = dune, method = "RawBeals")
-  ddBeals2 <- DarkDiv(x = dune, r = ddBeals$indication,  method = "RawBeals")
-  expect_equal(ddBeals, ddBeals2)
-  #Favorability
-  ddFav <- DarkDiv(x = dune, method = "Favorability")
-  ddFav2 <- DarkDiv(x = dune, r = ddFav$indication,  method = "Favorability")
-  expect_equal(ddFav, ddFav2)
-  #Hypergeometric
-  ddHyp <- DarkDiv(x = dune, method = "Hypergeometric")
-  ddHyp2 <- DarkDiv(x = dune, r = ddHyp$indication,  method = "Hypergeometric")
-  expect_equal(ddHyp, ddHyp2)
-})
-
-test_that("When removeAbsent = F, names of species and sites are unchanged, even if some species are removed", {
-  require(vegan)
-  data(dune)
-  dune2 <- dune
-  dune2[ , 2] <- rep(0, nrow(dune2))
-  #RawBeals
-  ddHypFull <- DarkDiv(x = dune, method = "Hypergeometric")
-  ddHypPart <- DarkDiv(x = dune2, method = "Hypergeometric", removeAbsent = F)
-  expect_equal(dimnames(ddHypFull$AllProbs), dimnames(ddHypPart$Pool))
-})
-
+library(testthat)
+library(DarkDiv)
+
+test_that("Beals gives same results as vegan", {
+  require(vegan)
+  data(dune)
+  BealsDD <- DarkDiv(x = dune, method = "RawBeals")
+  BealsVegan <- vegan::beals(x = dune, type = 0, include=F)
+  expect_equal(BealsDD$AllProbs, BealsVegan)
+})
+
+test_that("Using indication matrix directly yields same results as reference", {
+  require(vegan)
+  data(dune)
+  #RawBeals
+  ddBeals <- DarkDiv(x = dune, method = "RawBeals")
+  ddBeals2 <- DarkDiv(x = dune, r = ddBeals$indication,  method = "RawBeals")
+  expect_equal(ddBeals, ddBeals2)
+  #Favorability
+  ddFav <- DarkDiv(x = dune, method = "Favorability")
+  ddFav2 <- DarkDiv(x = dune, r = ddFav$indication,  method = "Favorability")
+  expect_equal(ddFav, ddFav2)
+  #Hypergeometric
+  ddHyp <- DarkDiv(x = dune, method = "Hypergeometric")
+  ddHyp2 <- DarkDiv(x = dune, r = ddHyp$indication,  method = "Hypergeometric")
+  expect_equal(ddHyp, ddHyp2)
+})
+
+test_that("When removeAbsent = F, names of species and sites are unchanged, even if some species are removed", {
+  require(vegan)
+  data(dune)
+  dune2 <- dune
+  dune2[ , 2] <- rep(0, nrow(dune2))
+  #RawBeals
+  ddHypFull <- DarkDiv(x = dune, method = "Hypergeometric")
+  ddHypPart <- DarkDiv(x = dune2, method = "Hypergeometric", removeAbsent = F)
+  expect_equal(dimnames(ddHypFull$AllProbs), dimnames(ddHypPart$Pool))
+})
+