Nothing
## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----setup, echo = FALSE------------------------------------------------------
suppressPackageStartupMessages(library(fmesher))
suppressPackageStartupMessages(library(tibble))
convert_fun_links <- function(df) {
webref <- list(
fmesher = "../reference/",
inlabru = "https://inlabru-org.github.io/inlabru/reference/"
)
for (k in seq_len(nrow(df))) {
df$INLA[[k]] <- paste0("`", df$INLA[[k]], "`")
df$fmesher[[k]] <-
vapply(
df$fmesher[[k]],
function(x) {
pkg_name <- sub(
pattern = "^(([^:]*)::)?([^(]+)(\\(.*\\))(<-)?$",
replacement = "\\2",
x = x
)
if (identical(pkg_name, "")) {
pkg_name <- "fmesher"
}
nm <- sub(
pattern = "^(([^:]*)::)?([^(]+)(\\(.*\\))(<-)?$",
replacement = "\\3",
x = x
)
args <- sub(
pattern = "^(([^:]*)::)?([^(]+)(\\(.*\\))(<-)?$",
replacement = "\\4\\5",
x = x
)
help_name <- basename(utils::help((nm), package = (pkg_name)))
paste0(
'<a href="', webref[[pkg_name]], help_name, '.html">`',
if (!identical(pkg_name, "fmesher")) {
paste0(pkg_name, "::")
} else {
""
},
nm,
args,
"`</a>"
)
},
""
)
}
df
}
## ----echo = FALSE-------------------------------------------------------------
df <- tribble(
~INLA, ~fmesher,
"inla.mesh.create()", c("fm_rcdt_2d()", "fm_rcdt_2d_inla()"),
"inla.mesh.2d()", c("fm_mesh_2d()", "fm_mesh_2d_inla()"),
"inla.delaunay()", "fm_delaunay_2d()",
"inla.mesh.1d()", "fm_mesh_1d()",
"inla.mesh.lattice()", "fm_lattice_2d()",
"inla.mesh.segment()", "fm_segm()",
"inla.nonconvex.hull()", c("fm_nonconvex_hull()", "fm_extensions()", "fm_simplify()"),
c(
"inla.nonconvex.hull()",
"inla.contour.segment()",
"inla.simplify.curve()"
),
c(
"fm_nonconvex_hull_inla()",
"fm_simplify_helper()",
"fm_segm_contour_helper()"
)
)
df <- convert_fun_links(df)
## ----echo = FALSE-------------------------------------------------------------
knitr::kable(df)
## ----echo = FALSE-------------------------------------------------------------
df <- tribble(
~INLA, ~fmesher,
"inla.mesh.projector()", "fm_evaluator()",
"inla.mesh.project()", "fm_evaluate()",
"inla.spde.make.A()", c(
"fm_basis()",
"fm_row_kron()",
"inlabru::bru_mapper_multi()",
"inlabru::ibm_jacobian()",
"fm_block()",
"fm_block_eval()",
"inlabru::bru_mapper_aggregate()"
),
"inla.mesh.deriv()", "fm_basis()"
)
df <- convert_fun_links(df)
## ----echo = FALSE-------------------------------------------------------------
knitr::kable(df)
## ----echo = FALSE-------------------------------------------------------------
df <- tribble(
~INLA, ~fmesher, ~Comment,
c("inla.mesh.fem()", "inla.mesh.1d.fem()"), "fm_fem()", " ",
" ", "fm_matern_precision()", " ",
" ", "fm_matern_sample()", "Convenience function that combines `fm_matern_precision()` and `fm_sample()`.",
" ", "fm_covariance()", "Basic helper function for compution covariances between different locations. Can produce sparse inverses like `inla.qinv()`, but currently (version 0.1.1) only by a 'brute force' method.",
" ", "fm_sample()", "Basic sampling method, like `inla.qsample()`"
)
df <- convert_fun_links(df)
## ----echo = FALSE-------------------------------------------------------------
knitr::kable(df)
## ----echo = FALSE-------------------------------------------------------------
df <- tribble(
~INLA,
~fmesher,
~Comments,
"summary.inla.mesh()",
c(
"print.fm_mesh_2d()",
"print.fm_segm()",
"print.fm_mesh_1d()"
),
"Use `print(mesh)` etc."
)
df <- convert_fun_links(df)
## ----echo = FALSE-------------------------------------------------------------
knitr::kable(df)
## ----echo = FALSE-------------------------------------------------------------
df <- convert_fun_links(
tibble::tribble(
~INLA, ~fmesher, ~Comments,
"inla.spTransform()", "fm_transform()", "",
"mesh$crs", c("fm_crs(mesh)", "fm_CRS(mesh)"), "The crs may now be stored in different formats; use `fm_crs()` for `sf` format, and `fm_CRS()` for `sp` format. `fmesher` will attempt to convert when needed.",
"mesh$crs<-", "fm_crs(mesh)<-", "Direct assignment of crs information should be avoided, but is allowed as long as its compatible with the actual mesh coordinates."
)
)
## ----echo = FALSE-------------------------------------------------------------
knitr::kable(df)
## ----echo = FALSE-------------------------------------------------------------
df <- tribble(
~INLA, ~fmesher, ~Comment,
"No ggplot support", c("geom_fm(data = mesh)", "geom_fm(data = segm)"), "Use `ggplot() + geom_fm(data = mesh)` and `inlabru::gg()` methods",
"plot.inla.mesh(rgl = FALSE)", c("plot.fm_mesh_2d()", "lines.fm_mesh_2d()"), "Use `plot()` or `lines()`",
"lines.inla.mesh.segment(rgl = FALSE)", c(
"plot.fm_segm()",
"lines.fm_segm()"
), "Use `plot()` or `lines()`",
"plot.inla.mesh(rgl = TRUE)", c("plot_rgl()", "lines_rgl()"), "",
"lines.inla.mesh.segment(rgl = TRUE)", c(
"plot_rgl()",
"lines_rgl()"
),
""
)
df <- convert_fun_links(df)
## ----echo = FALSE-------------------------------------------------------------
knitr::kable(df)
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