Merge branch 'cran-3.0-9-fixes'

Author: jarioksa

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: Hmsc
 Title: Hierarchical Model of Species Communities
 Type: Package
-Version: 3.0-8
+Version: 3.0-9
 Authors@R: c(person(given = "Gleb", family="Tikhonov", role="aut"),
    person(given="Otso", family="Ovaskainen",
       email="otso.ovaskainen@helsinki.fi",
@@ -13,9 +13,10 @@ Authors@R: c(person(given = "Gleb", family="Tikhonov", role="aut"),
 Description: Hierarchical Modelling of Species Communities (HMSC) is
    a model-based approach for analyzing community ecological data. 
    This package implements it in the Bayesian framework with Gibbs
-   Markov chain Monte Carlo (MCMC) sampling.
+   Markov chain Monte Carlo (MCMC) sampling (Tikhonov et al. (2020)
+   <doi:10.1111/2041-210X.13345>).
 License: GPL-3 | file LICENSE
-URL: https://www.helsinki.fi/en/researchgroups/statistical-ecology/hmsc/
+URL: https://www.helsinki.fi/en/researchgroups/statistical-ecology/hmsc
 BugReports: https://github.com/hmsc-r/HMSC/issues/
 Encoding: UTF-8
 LazyData: true

R/constructGradient.R

@@ -17,14 +17,13 @@
 #' \code{type = 2} sets the values of the non-focal variable to most likely value, given the value of focal variable,
 #' based on a linear relationship, and
 #' \code{type = 3} fixes to the value given.
-#' If all non-focal variables are of the identical \code{type} \code{1} or \code{2},
-#' a single number (\code{1} or \code{2}) can be given as an argument to
-#' \code{non.focalVariables}.
+#' As a shortcut, a single number \code{1} or \code{2} can be given as a type
+#' used for all non-focal variables.
 #' If a \code{non.focalVariable} is not listed, \code{type=2} is used as default.
 #' Note that if the focal variable is continuous, selecting type 2 for a non-focal categorical variable can cause abrupt changes in response.
 #'
 #' @seealso
-#' \code{\link{plotGradient}}, \code{\link{predict}}
+#' \code{\link{plotGradient}}, \code{\link{predict}}.
 #'
 #' @examples
 #' # Construct gradient for environmental covariate called 'x1'.

inst/NEWS.md

@@ -1,4 +1,4 @@
-Version 3.0-8
+Version 3.0-9
 =============
 
 ### Installation
@@ -43,6 +43,18 @@ Version 3.0-8
   species. See GitHub
   [issue #44](https://github.com/hmsc-r/HMSC/issues/44).
 
+* `constructGradient` argument `nonFocalVariables` accepts now a
+  single number `1` or `2` as a shortcut of default type for all
+  non-focal variables instead of requesting a list of types of all
+  variables.
+
+* `plotGradient` gained new argument `yshow` which is a single number
+  or vector of numeric values that must be included on the
+  *y*-axis. In general, the *y*-axis is scaled to show the plotted
+  values, but `yshow = 0` will always show zero, even when this is not
+  among plotted values, and `yshow = c(0,1)` will show both zero and
+  one.
+
 * `plotVariancePartition` defaults to plot the original terms instead
   of single contrast. For instance, only one component is shown for
   multilevel factors instead of showing each level separately. User
@@ -68,7 +80,9 @@ Version 3.0-8
 
 * `plotGradient(..., showData = TRUE)` ignored data values in setting
   plot minimum. See GitHub
-  [issue #48](https://github.com/hmsc-r/HMSC/issues/48).
+  [issue #48](https://github.com/hmsc-r/HMSC/issues/48). The data
+  values were not always shown with `measure = "S"` in quantitative
+  linear models.
 
 Version 3.0-6
 =============

man/Hmsc-package.Rd

@@ -85,13 +85,16 @@ Hierarchical Modelling of Species Communities (Hmsc) is a
 }
 
 \section{Citing the Package}{
- Tikhonov, G., Opedal, O., Abrego, N., Lehikoinen, A., Ovaskainen, O., 2019. Joint species distribution modelling with HMSC-R. \emph{bioRxiv}
+  Tikhonov, G., Opedal, O.H., Abrego, N., Lehikoinen, A., de Jonge,
+  M.M.J, Oksanen, J. and Ovaskainen, O. (2020) Joint species
+  distribution modelling with the R-package Hmsc. \emph{Methods in
+  Ecology and Evolution} \bold{11,} 442--447. \doi{10.1111/2041-210X.13345}
 }
 
 \seealso{
 Useful links:
 \itemize{
-  \item \url{https://www.helsinki.fi/en/researchgroups/statistical-ecology/hmsc/}
+  \item \url{https://www.helsinki.fi/en/researchgroups/statistical-ecology/hmsc}
   \item Report bugs at \url{https://github.com/hmsc-r/HMSC/issues/}
 }