From a19d71774a1d94c07e21a0cd20d03a8674a95b4c Mon Sep 17 00:00:00 2001
From: rsetienne <rampaletienne@gmail.om>
Date: Sat, 21 Oct 2023 15:54:34 +0200
Subject: [PATCH] Documentation

---
 R/DAISIE_loglik_integrate.R | 12 ++++++------
 man/DAISIE-package.Rd       |  1 +
 man/integral_peak.Rd        | 11 ++++++-----
 3 files changed, 13 insertions(+), 11 deletions(-)

diff --git a/R/DAISIE_loglik_integrate.R b/R/DAISIE_loglik_integrate.R
index 90367a69..860b4264 100644
--- a/R/DAISIE_loglik_integrate.R
+++ b/R/DAISIE_loglik_integrate.R
@@ -145,11 +145,11 @@ cum_rho <- function(par_upper_bound, DAISIE_dist_pars) {
 #' @description computes the logarithm of the integral of exp(logfun) from 0
 #' to Inf under the following assumptions:
 #' \itemize{
-#'  \item{"exp(logfun)"}{has a single, sharply peaked maximum}
-#'  \item{"exp(logfun)"}{is increasing to the left of the peak and
+#'  \item{"exp(logfun)" has a single, sharply peaked maximum}
+#'  \item{"exp(logfun)" is increasing to the left of the peak and
 #'  decreasing to the right of the peak}
-#'  \item{"exp(logfun)"}{can be zero or positive at zero}
-#'  \item{"exp(logfun)"}{tends to zero at infinity}
+#'  \item{"exp(logfun)" can be zero or positive at zero}
+#'  \item{"exp(logfun)" tends to zero at infinity}
 #' }
 #' @param logfun the logarithm of the function to integrate
 #' @param xx the initial set of points on which to evaluate the function
@@ -159,9 +159,9 @@ cum_rho <- function(par_upper_bound, DAISIE_dist_pars) {
 #' among the xx
 #' @return the result of the integration
 #' @references Haegeman, B. & R.S. Etienne (2017). A general sampling formula
-#' for community structure data. Methods in Ecology & Evolution. In press.
+#' for community structure data. Methods in Ecology & Evolution 8: 1506-1519.
+#' https://doi.org/10.1111/2041-210X.12807
 #' @keywords internal
-#'
 integral_peak <- function(logfun,
                           xx = seq(-20, 20, 2),
                           xcutoff = 2,
diff --git a/man/DAISIE-package.Rd b/man/DAISIE-package.Rd
index 92fc8d31..05e1a746 100644
--- a/man/DAISIE-package.Rd
+++ b/man/DAISIE-package.Rd
@@ -33,6 +33,7 @@ Cladogenesis and immigration rates can be dependent on diversity.
 Useful links:
 \itemize{
   \item \url{https://github.com/rsetienne/DAISIE}
+  \item \url{https://rsetienne.github.io/DAISIE/}
   \item Report bugs at \url{https://github.com/rsetienne/DAISIE/issues}
 }
 
diff --git a/man/integral_peak.Rd b/man/integral_peak.Rd
index 0234e6fe..edcae22c 100644
--- a/man/integral_peak.Rd
+++ b/man/integral_peak.Rd
@@ -43,15 +43,16 @@ the result of the integration
 computes the logarithm of the integral of exp(logfun) from 0
 to Inf under the following assumptions:
 \itemize{
- \item{"exp(logfun)"}{has a single, sharply peaked maximum}
- \item{"exp(logfun)"}{is increasing to the left of the peak and
+ \item{"exp(logfun)" has a single, sharply peaked maximum}
+ \item{"exp(logfun)" is increasing to the left of the peak and
  decreasing to the right of the peak}
- \item{"exp(logfun)"}{can be zero or positive at zero}
- \item{"exp(logfun)"}{tends to zero at infinity}
+ \item{"exp(logfun)" can be zero or positive at zero}
+ \item{"exp(logfun)" tends to zero at infinity}
 }
 }
 \references{
 Haegeman, B. & R.S. Etienne (2017). A general sampling formula
-for community structure data. Methods in Ecology & Evolution. In press.
+for community structure data. Methods in Ecology & Evolution 8: 1506-1519.
+https://doi.org/10.1111/2041-210X.12807
 }
 \keyword{internal}