Update documentation DAISIE_logp0 and related chances in other functi…

…ons.

R/DAISIE_loglik_CS.R

@@ -1429,6 +1429,15 @@ logcondprob <- function(numcolmin, numimm, logp0, fac = 2) {
 #' @description Computes the log probability of no species present under the DAISIE
 #' model with clade-specific diversity-dependence. The output is a log value.
 #' @inheritParams default_params_doc
+#' #' @param pars2 Contains the model settings \cr \cr
+#' \code{pars2[1]} corresponds to lx = length of ODE variable x \cr
+#' \code{pars2[2]} corresponds to ddmodel = diversity-dependent model, model of diversity-dependence, which can be one
+#' of\cr \cr
+#' ddmodel = 0 : no diversity dependence \cr
+#' ddmodel = 1 : linear dependence in speciation rate \cr
+#' ddmodel = 11: linear dependence in speciation rate and in immigration rate \cr
+#' ddmodel = 2 : exponential dependence in speciation rate\cr
+#' ddmodel = 21: exponential dependence in speciation rate and in immigration rate\cr\cr
 #' @param island_age the island age \cr
 #' @return The logarithm of the probability
 #' @author Rampal S. Etienne & Bart Haegeman

tests/testthat/test-DAISIE_loglik_CS.R

@@ -24,8 +24,7 @@ test_that("DAISIE_loglik_CS_choice produces correct output for relaxed-rate
   skip_if(Sys.getenv("CI") == "", message = "Run only on CI")
   skip_on_cran()
   pars1 <- c(2.000, 2.700, 20.000, 0.009, 1.010)
-  pars2 <- c(1.0e+02, 1.1e+01, 0.0e+00, 0.0e+00, NA, 0.0e+00, 1.0e-04,
-             1.0e-05, 1.0e-07, 3.0e+03, 9.5e-01, 9.8e-01)
+  pars2 <- c(1.0e+02, 1.1e+01, 0.0e+00, 0.0e+00)
   brts <- c(4.0000, 3.0282, 1.3227, 0.8223, 0.4286, 0.3462, 0.2450, 0.0808,
             0.0527, 0.0327, 0.0221, 0.1180, 0.0756, 0.0525, 0.0322, 0.0118)
   stac <- 2
@@ -51,8 +50,7 @@ test_that("DAISIE_loglik_CS_choice produces same output for CS_version = 0
   skip_on_cran()
   skip_if(Sys.getenv("CI") == "", message = "Run only on CI")
   pars1 <- c(2.000, 2.700, 20.000, 0.009, 1.010)
-  pars2 <- c(100, 11, 0, 0, NA, 0.0e+00, 1.0e-04,
-             1.0e-05, 1.0e-07, 3.0e+03, 9.5e-01, 9.8e-01)
+  pars2 <- c(100, 11, 0, 0)
   brts <- c(4.0000, 3.0282, 1.3227, 0.8223, 0.4286, 0.3462, 0.2450, 0.0808,
             0.0527, 0.0327, 0.0221, 0.1180, 0.0756, 0.0525, 0.0322, 0.0118)
   stac <- 2
@@ -168,8 +166,7 @@ test_that("DAISIE_loglik_CS_choice produces equivalent output for ODEINT RKCK54
   skip_if(Sys.getenv("CI") == "", message = "Run only on CI")
   skip_on_cran()
   pars1 <- c(2.000, 2.700, 20.000, 0.009, 1.010)
-  pars2 <- c(1.0e+02, 1.1e+01, 0.0e+00, 0.0e+00, NA, 0.0e+00, 1.0e-04,
-             1.0e-05, 1.0e-07, 3.0e+03, 9.5e-01, 9.8e-01)
+  pars2 <- c(1.0e+02, 1.1e+01, 0.0e+00, 0.0e+00, NA)
   brts <- c(4.0000, 3.0282, 1.3227, 0.8223, 0.4286, 0.3462, 0.2450, 0.0808,
             0.0527, 0.0327, 0.0221, 0.1180, 0.0756, 0.0525, 0.0322, 0.0118)
   stac <- 2
@@ -195,8 +192,7 @@ test_that("DAISIE_loglik_CS_choice produces equivalent output for ODEINT RKCK54
 test_that("DAISIE_loglik_CS_choice produces equivalent
           output for ODEINT RKF78 and deSolve lsodes", {
   pars1 <- c(2.000, 2.700, 20.000, 0.009, 1.010)
-  pars2 <- c(1.0e+02, 1.1e+01, 0.0e+00, 0.0e+00, NA, 0.0e+00, 1.0e-04,
-             1.0e-05, 1.0e-07, 3.0e+03, 9.5e-01, 9.8e-01)
+  pars2 <- c(1.0e+02, 1.1e+01, 0.0e+00, 0.0e+00, NA)
   brts <- c(4.0000, 3.0282, 1.3227, 0.8223, 0.4286, 0.3462, 0.2450, 0.0808,
             0.0527, 0.0327, 0.0221, 0.1180, 0.0756, 0.0525, 0.0322, 0.0118)
   stac <- 2

tests/testthat/test-DAISIE_logp0.R

@@ -1,7 +1,6 @@
 test_that("DAISIE_logp0 is correct", {
   pars1 <- c(2.000, 2.700, 20.000, 0.009, 1.010)
-  pars2 <- c(1.0e+02, 1.1e+01, 0.0e+00, 0.0e+00, NA, 0.0e+00, 1.0e-04,
-             1.0e-05, 1.0e-07, 3.0e+03, 9.5e-01, 9.8e-01)
+  pars2 <- c(1.0e+02, 1.1e+01)
   island_age <- 4
   logp0 <- DAISIE_logp0(pars1 = pars1,
                         pars2 = pars2,