Merge branch 'master' into make_pkgdown

DESCRIPTION

@@ -2,31 +2,27 @@ Package: Distance
 License: GPL (>= 2)
 Title: Distance Sampling Detection Function and Abundance Estimation
 LazyLoad: yes
-Authors@R: 
-  c(person(given="David Laurence",
-           family="Miller",
-           role="aut"),
-    person(given="T.J.",
-           family="Clark-Wolf",
-           role="aut"),
-    person(given="Laura",
-           family="Marshall",
-           role="cre",
-           email="[email protected]"))
+Authors@R: c(
+  person("Laura", "Marshall", email = "[email protected]" , role = "cre"),
+  person("David", "Miller", email = "[email protected]", role = "aut"),
+  person("T.J.", "Clark-Wolf", role = "aut"),
+  person("Len", "Thomas", email = "[email protected]", role = "ctb"),
+  person("Jeff", "Laake", role = "ctb"),
+  person("Eric", "Rexstad", email = "[email protected]", role = "rev"))
 Description: A simple way of fitting detection functions to distance sampling
     data for both line and point transects. Adjustment term selection, left and
     right truncation as well as monotonicity constraints and binning are
     supported. Abundance and density estimates can also be calculated (via a
     Horvitz-Thompson-like estimator) if survey area information is provided. See
     Miller et al. (2019) <doi:10.18637/jss.v089.i01> for more information on
     methods and <https://examples.distancesampling.org/> for example analyses.
-Version: 1.0.9
+Version: 2.0.0
 URL: https://github.com/DistanceDevelopment/Distance/
 BugReports: https://github.com/DistanceDevelopment/Distance/issues
 Language: en-GB
 Depends:
     R (>= 3.5.0),
-    mrds (>= 2.3.0)
+    mrds (>= 3.0.0)
 Imports:
     dplyr,
     methods,
@@ -44,4 +40,4 @@ Suggests:
     readxl
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2

NEWS.md

@@ -1,3 +1,8 @@
+# Distance 2.0.0
+
+* Requires mrds 3.0.0. mrds is called by ds for fitting detection functions. In mrds there has been a change of optimizer used for CDS detection functions - a constraint solver slsqp now used. This removes the need for external optimizer MCDS.exe in most cases. Other minor changes to optimization have been implemented to improve reliability (see NEWS file of mrds for more info).
+* New argument mono_method added so that the previous constraint solver (solnp) can still be used. MCDS.exe is also still available if needed.
+
 # Distance 1.0.9
 
 * Changed the default encounter rate estimator for point transect surveys from P3 to P2. (Issue #138)

R/Distance-package.R

@@ -12,13 +12,15 @@
 #'
 #' For help with distance sampling and this package, there is a Google Group
 #' <https://groups.google.com/forum/#!forum/distance-sampling>.
+#' 
+#' Bugs can be reported at <https://github.com/DistanceDevelopment/Distance/issues>.
 #'
 #' @name Distance-package
 #' @import mrds
 #' @aliases Distance-package Distance
-#' @docType package
 #' @author David L. Miller <dave@@ninepointeightone.net>
 #' @references
+#' "_PACKAGE"
 #'
 #' Key References:
 #'

R/ds.R

@@ -100,6 +100,8 @@
 #' @param method optimization method to use (any method usable by
 #' [`optim`][stats::optim] or [`optimx`][optimx::optimx]). Defaults to
 #' `"nlminb"`.
+#' @param mono_method optimization method to use when monotonicity is enforced. 
+#' Can be either `slsqp` or `solnp`. Defaults to `slsqp`.
 #' @param debug_level print debugging output. `0`=none, `1-3` increasing levels
 #' of debugging output.
 #' @param quiet suppress non-essential messages (useful for bootstraps etc).
@@ -255,9 +257,9 @@
 #' density estimates made with the `Area` column present.
 #'
 #' @author David L. Miller
-#' @seealso [`flatfile`][flatfile], [`AIC.ds`][AIC.ds], [`ds.gof`][ds.gof],
-#' [`p_dist_table`][p_dist_table], [`plot.ds`][plot.ds],
-#' [`add_df_covar_line`][add_df_covar_line]
+#' @seealso \code{\link{flatfile}}, \code{\link[mrds]{AIC.ds}}, 
+#' \code{\link{ds.gof}}, \code{\link{p_dist_table}}, 
+#' \code{\link[mrds]{plot.ds}}, \code{\link{add_df_covar_line}}
 #' @export
 #'
 #' @importFrom stats quantile as.formula
@@ -334,7 +336,9 @@ ds <- function(data, truncation=ifelse(is.null(cutpoints),
              monotonicity=ifelse(formula==~1, "strict", "none"),
              region_table=NULL, sample_table=NULL, obs_table=NULL,
              convert_units=1, er_var=ifelse(transect=="line", "R2", "P2"),
-             method="nlminb", quiet=FALSE, debug_level=0,
+             method="nlminb", 
+             mono_method = "slsqp", # FTP: new slot to specify the constraint R solver
+             quiet=FALSE, debug_level=0,
              initial_values=NULL, max_adjustments=5, er_method=2, dht_se=TRUE,
              optimizer = "both",
              winebin = NULL,
@@ -521,6 +525,7 @@ ds <- function(data, truncation=ifelse(is.null(cutpoints),
 
   # set up the control options
   control <- list(optimx.method=method, showit=debug_level,
+                  mono.method = mono_method, ## FTP: again, this is needed
                   optimizer = optimizer, winebin = winebin)
 
   # if initial values were supplied, pass them on
@@ -719,8 +724,8 @@ ds <- function(data, truncation=ifelse(is.null(cutpoints),
   }
 
   # check to see if resulting function is monotonic
-  mono.chk <- mrds::check.mono(model, n.pts=20)
-
+  mono.chk <- mrds::check.mono(model, n.pts=10) # FTP: n.pts was 20, now 10 to match the solver in mrds.
+  
   ## Now calculate abundance/density using dht()
   if(!is.null(region_table) & !is.null(sample_table)){
     # if obs_table is not supplied, then data must have the Region.Label and

R/print.summary.dsmodel.R

@@ -9,7 +9,7 @@
 #' @param \dots unspecified and unused arguments for S3 consistency
 #' @return Nothing, just prints the summary.
 #' @author David L. Miller and Jeff Laake
-#' @seealso [`summary.ds`][summary.ds]
+#' @seealso \code{\link[mrds]{summary.ds}}
 #' @keywords utility
 #' @export
 print.summary.dsmodel <- function (x,...){

R/summary.dsmodel.R

@@ -8,7 +8,7 @@
 #' @param object a distance analysis
 #' @param \dots unspecified and unused arguments for S3 consistency
 #' @return list of extracted and summarized objects
-#' @note This function just calls [`summary.ds`][summary.ds] and [`dht`][dht],
+#' @note This function just calls \code{\link[mrds]{summary.ds}} and \code{\link[mrds]{dht}},
 #' collates and prints the results in a nice way.
 #' @author David L. Miller
 #' @keywords utility

tests/testthat/test_summarize.R

@@ -24,12 +24,12 @@ test_that("Error on different truncation distance", {
   out <- read.table(text="
 \\texttt{t4}                                              Half-normal      ~1    0.7789695         0.5842744       0.04637627         0.000000
 \\texttt{t42}                                             Half-normal      ~1    0.7789695         0.5842744       0.04637627         0.000000
-\\texttt{t4hr} \"Hazard-rate with cosine adjustment term of order 2\"      ~1    0.8170780         0.5556728       0.07197555         2.501712
+\\texttt{t4hr} \"Hazard-rate with cosine adjustment term of order 2\"      ~1    0.8162846         0.5543305       0.07156778         2.454826
 ", header=FALSE)
   names(out) <- c("Model", "Key function", "Formula", "C-vM p-value",
                 "$\\hat{P_a}$", "se($\\hat{P_a}$)", "$\\Delta$AIC")
   expect_equal(summarize_ds_models(t4, t42, t4hr), out, fixed=TRUE, tol=par.tol)
-
+  
   # right truncation different
   expect_error(summarize_ds_models(t3, t4))
   # left