test

Merge branch 'main' of https://github.com/gamlss-dev/gamlss2

# Conflicts:
#	vignettes/families.Rmd

.Rbuildignore

@@ -3,12 +3,10 @@ inst/tests.qmd
 inst/SGT.R
 inst/OpenTopics.qmd
 token
-random.Rmd 
-selection.Rmd 
-spatial.Rmd
-s_pb.Rmd 
-topmodels.Rmd
+README.qmd
 .github
 ^_quarto$
 ^altdoc$
 ^docs$
+^.*\.Rproj$
+^\.Rproj\.user$

.gitignore

@@ -3,12 +3,11 @@
 .Rhistory
 .Rapp.history
 .Rproj.user/
-
 # vignette output
 vignettes/*.html
 vignettes/*.pdf
-
 # altdoc infrastructure
 altdoc/freeze.rds
 _quarto/
 docs/
+.Rbuildignore

DESCRIPTION

@@ -19,7 +19,7 @@ URL: https://gamlss-dev.github.io/gamlss2/
 BugReports: https://github.com/gamlss-dev/gamlss2/issues
 Depends: R (>= 4.1.0), gamlss.dist, mgcv
 Imports: parallel, Formula, mvtnorm
-Suggests: gamlss, gamlss.data, colorspace, knitr, scoringRules, partykit, Matrix, nnet, lattice, rpart, distributions3, nlme
+Suggests: gamlss, gamlss.data, colorspace, ggplot2, knitr, scoringRules, partykit, Matrix, nnet, lattice, rpart, distributions3, nlme, sf, spdep
 LazyLoad: yes
 VignetteBuilder: knitr
 

NAMESPACE

@@ -46,7 +46,8 @@ export(
   "new_formula",
   "softplus",
   "shiftlog",
-  "Kumaraswamy"
+  "Kumaraswamy",
+  "make.link2"
 )
 
 S3method(gamlss2, formula)

R/specials.R

@@ -98,6 +98,16 @@ special_terms <- function(x, data, binning = FALSE, digits = Inf, ...)
     }
   }
 
+  if(any(dups <- duplicated(names(sterms)))) {
+    dups <- names(sterms)[dups]
+    for(j in dups) {
+      dn <- grep(j, names(sterms), fixed = TRUE, value = TRUE)
+      dn <- paste0(dn, ".", 1:length(dn))
+      i <-  grep(j, names(sterms), fixed = TRUE)
+      names(sterms)[i] <- dn
+    }
+  }
+
   return(sterms)
 }
 

README.md

@@ -1,45 +1,37 @@
-
-
-# gamlss2: Infrastructure for  Distributional Regression
+# gamlss2: GAMLSS Infrastructure for Flexible Distributional Regression
 
 ## Installation
 
-The development version of *gamlss2* can be installed via
+The development version of _gamlss2_ can be installed via
 
-``` r
+```{r installation, eval = FALSE}
 install.packages("gamlss2",
   repos = c("https://gamlss-dev.R-universe.dev", "https://cloud.R-project.org"))
 ```
 
-## Overview
-
-The primary purpose of this package is to facilitate the creation of
-advanced infrastructures designed to enhance the GAMLSS modeling
-framework. Notably, the *gamlss2* package represents a significant
-overhaul of its predecessor, *gamlss*, with a key emphasis on improving
-estimation speed and incorporating more flexible infrastructures. These
-enhancements enable the seamless integration of various algorithms into
-GAMLSS, including gradient boosting, Bayesian estimation, regression
-trees, and forests, fostering a more versatile and powerful modeling
-environment.
-
-Moreover, the package expands its compatibility by supporting all model
-terms from the base R *mgcv* package. Additionally, the *gamlss2*
-package introduces the capability to accommodate more than four
-parameter families. Essentially, this means that users can now specify
-any type of model using these new infrastructures, making the package
-highly flexible and accommodating to a wide range of modeling
-requirements.
-
--   The main model function is `gamlss2()`.
--   The default optimizer functions is `RS()`. Optimizer functions can
-    be exchanged.
--   Most important methods: `summary()`, `plot()`, `predict()`.
--   Easy development of new family objects, see `?family.gamlss2`.
--   User-specific “special” terms are possible, see `?special_terms`.
+## Overview 
+
+The primary purpose of this package is to facilitate the creation of advanced infrastructures
+designed to enhance the GAMLSS modeling framework. Notably, the _gamlss2_ package represents a
+significant overhaul of its predecessor, _gamlss_, with a key emphasis on improving estimation
+speed and incorporating more flexible infrastructures. These enhancements enable the seamless
+integration of various algorithms into GAMLSS, including gradient boosting, Bayesian estimation,
+regression trees, and forests, fostering a more versatile and powerful modeling environment.
+
+Moreover, the package expands its compatibility by supporting all model terms from the base
+R _mgcv_ package. Additionally, the _gamlss2_ package introduces the capability to
+accommodate more than four parameter families. Essentially, this means that users can now
+specify any type of model using these new infrastructures, making the package highly
+flexible and accommodating to a wide range of modeling requirements.
+
+* The main model function is `gamlss2()`.
+* The default optimizer functions is `RS()`. Optimizer functions can be exchanged.
+* Most important methods: `summary()`, `plot()`, `predict()`.
+* Easy development of new family objects, see `?family.gamlss2`.
+* User-specific "special" terms are possible, see `?special_terms`.
 
 For examples, please visit the manual pages.
 
-``` r
+```{r help, eval = FALSE}
 help(package = "gamlss2")
 ```

inst/extra/GermanyElevation.grd

@@ -0,0 +1,27 @@
+[general]
+creator=R package 'raster'
+created=2024-09-30 08:52:19
+[data]
+datatype=FLT4S
+byteorder=little
+nbands=1
+bandorder=BIL
+categorical=FALSE
+minvalue=-33
+maxvalue=1992
+nodatavalue=-3.4e+38
+[legend]
+legendtype=
+values=
+color=
+[description]
+layername=file29ba723b9492a
+[georeference]
+nrows=209
+ncols=246
+xmin=5.87622623088577
+ymin=47.2597641144092
+xmax=15.0252873245434
+ymax=55.0327469134923
+projection=+proj=longlat +datum=WGS84 +no_defs
+wkt=GEOGCRS["unknown",    DATUM["World Geodetic System 1984",        ELLIPSOID["WGS 84",6378137,298.257223563,            LENGTHUNIT["metre",1]],        ID["EPSG",6326]],    PRIMEM["Greenwich",0,        ANGLEUNIT["degree",0.0174532925199433],        ID["EPSG",8901]],    CS[ellipsoidal,2],        AXIS["longitude",east,            ORDER[1],            ANGLEUNIT["degree",0.0174532925199433,                ID["EPSG",9122]]],        AXIS["latitude",north,            ORDER[2],            ANGLEUNIT["degree",0.0174532925199433,                ID["EPSG",9122]]]]

man/Germany.Rd

@@ -0,0 +1,47 @@
+\name{Germany}
+\alias{Germany}
+
+\encoding{UTF-8}
+
+\title{Map of Germany}
+
+\description{
+  The map contains the counties of Germany. The data was originally taken from
+  GADM (\url{https://gadm.org/}) and slightly simplified to reduce disk space.
+}
+
+\usage{data("storms", package = "gamlss2")}
+
+\format{
+A class \code{"sf"} data frame containing 403 counties of Germany.
+\describe{
+  \item{id}{Factor, a county id.}
+  \item{county}{Character, the county in Germany where the weather station is located.}
+  \item{state}{Character, the state in Germany where the weather station is located.}
+  \item{geometry}{The polygon information.}
+}
+}
+
+\source{
+  Map of Germany:
+  \describe{
+    \item{Data Source:}{GADM}
+    \item{Licence:}{CC BY}
+    \item{URL:}{\url{https://gadm.org/}}
+    \item{Coordinate Reference System:}{Longitude/latitude and the WGS84 datum.}
+  }
+}
+
+\examples{\dontshow{ if(!requireNamespace("sf")) { if(interactive() || is.na(Sys.getenv("_R_CHECK_PACKAGE_NAME_", NA))) { stop("not all packages required for the example are installed") } else q() }}
+## load sf package for plotting
+library("sf")
+
+## load the data
+data("Germany", package = "gamlss2")
+
+## plot the map
+plot(st_geometry(Germany))
+}
+
+\keyword{datasets}
+

man/make.link2.Rd

@@ -0,0 +1,44 @@
+\name{make.link2}
+\alias{make.link2}
+
+\title{Create a Link for Families}
+
+\description{
+  This function is used with the \code{family} functions in \code{gamlss2()}.
+  Given the name of a link, it returns a link function, an inverse
+  link function, the derivative \eqn{d\mu/d\eta}, and a function for domain
+  checking. Note that \code{make.link2()} is slightly more flexible and also allows
+  functions as arguments.
+}
+
+\usage{
+make.link2(link)
+}
+
+\arguments{
+  \item{link}{
+    A character string, see function \code{\link[stats]{make.link}}, or function.
+  }
+}
+
+\value{
+  A list containing the following components:
+  \item{linkfun}{Link function \code{function(mu)}.}
+  \item{linkinv}{Inverse link function \code{function(eta)}.}
+  \item{mu.eta}{Derivative \code{function(eta)}: \eqn{d\mu/d\eta}.}
+  \item{valideta}{Function \code{function(eta)} that returns \code{TRUE} if \code{eta} is in the domain of \code{linkinv}.}
+  \item{name}{A character string representing the name of the link function.}
+}
+
+\seealso{
+  \code{\link[stats]{make.link}}, \code{\link{gamlss2}}, \code{\link{gamlss2.family}}.
+}
+
+\examples{
+## character specification
+utils::str(make.link2("logit"))
+
+## functions
+utils::str(make.link2(softplus))
+}
+

man/storms.Rd

@@ -0,0 +1,66 @@
+\name{storms}
+\alias{storms}
+
+\encoding{UTF-8}
+
+\title{Severe Storms in Germany}
+
+\description{
+  According to the Beaufort scale, severe storms occur from a wind speed of 24.5-28.4 m/s.
+  This dataset contains annual severe storm counts from weather stations in Germany
+  from 1981 to 2021.
+}
+
+\usage{data("storms", package = "gamlss2")}
+
+\format{
+A data frame containing 3494 observations on 8 variables.
+\describe{
+  \item{id}{Factor, the weather station id.}
+  \item{county}{Character, the county in Germany where the weather station is located.}
+  \item{state}{Character, the state in Germany where the weather station is located.}
+  \item{year}{Integer, the year the observation was measured.}
+  \item{counts}{Integer, the number of severe storms in this year.}
+  \item{alt}{Numeric, the altitude in meters above sea level of the weather station.}
+  \item{lon}{Numeric, the longitude coordinate of the weather station.}
+  \item{lat}{Numeric, the latitude coordinate of the weather station.}
+}
+}
+
+\source{
+  Severe Storms Data:
+  \describe{
+    \item{Data Source:}{Deutscher Wetterdienst (DWD), Climate Data Center (CDC).}
+    \item{Licence:}{CC BY 4.0}
+    \item{URL:}{\url{https://opendata.dwd.de/climate_environment/CDC/}}
+    \item{Coordinate Reference System:}{Longitude/latitude and the WGS84 datum.}
+  }
+}
+
+\examples{
+## load the data
+data("storms", package = "gamlss2")
+
+## yearly observations
+plot(counts ~ year, data = storms)
+
+## count distribution
+barplot(table(storms$counts))
+
+## NBI model
+## model formula including spatial effect
+\dontrun{f <- counts ~ s(year) + s(alt) + s(lon, lat) |
+  s(year) + s(alt) + s(lon, lat)
+
+## estimate model
+b <- gamlss2(f, data = storms, family = NBI)
+
+## estimated effects
+plot(b)
+
+## residual diagnostics
+plot(b, which = "resid")
+}}
+
+\keyword{datasets}
+