From 35ffcc4031d18c4d08752ae9c600cca3a1184d53 Mon Sep 17 00:00:00 2001
From: Jean-Matthieu Monnet <jean-matthieu.monnet@inrae.fr>
Date: Tue, 21 Jan 2025 13:30:13 +0100
Subject: [PATCH] ... arguments added to some functions, no-finite values
replaced in aba
---
DESCRIPTION | 4 ++--
NEWS.md | 3 +++
R/aba.R | 19 ++++++++++++++-----
R/optical_metrics.R | 2 +-
README.md | 4 ++--
man/aba_build_model.Rd | 9 +++++++--
man/aba_predict.Rd | 5 ++++-
man/add_vegetation_indices.Rd | 2 +-
man/convert_raster.Rd | 11 ++---------
9 files changed, 36 insertions(+), 23 deletions(-)
diff --git a/DESCRIPTION b/DESCRIPTION
index ca1adbb..1044ce6 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: lidaRtRee
Type: Package
Version: 4.0.7
Title: Forest Analysis with Airborne Laser Scanning (LiDAR) Data
-Date: 2024-03-13
+Date: 2024-09-13
Authors@R: c(
person("Jean-Matthieu", "Monnet", email = "jean-matthieu.monnet@inrae.fr", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9948-9891")),
person("Pascal", "Obstétar", email = "pascal.obstetar@onf.fr", role = c("ctb"), comment = c(ORCID = "0000-0002-2811-7548")))
@@ -24,5 +24,5 @@ Imports: graphics, stats, methods, grDevices, terra, sf, imager, leaps, gvlma, c
Suggests: stars
License: GPL-3
LazyData: TRUE
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
Encoding: UTF-8
diff --git a/NEWS.md b/NEWS.md
index 3c40bde..3aac860 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -3,11 +3,14 @@
## New
* `clouds_tree_metrics()` now has a `roi` argument to select trees to retain for subsequent computation based on spatial object.
+* `ABA_predict()` now has a `...` argument to pass additional arguments to `stats::predict.lm()`.
## Change
* `boxcox_tr()` and `boxcox_itr()` do not automatically replace `0` with `NA` anymore.
* `RasterLayer` objects are not supported anymore as the `raster` package package is now obsolete.
+* in `aba_build_model()`, when specified the minimum `threshold` parameter now replaces non finite values in predictions.
+* added `...` argument in `aba_build_model()`: passed to `leaps::regsubsets()`
# lidaRtRee 4.0.6
diff --git a/R/aba.R b/R/aba.R
index 435d1da..9dd6f99 100755
--- a/R/aba.R
+++ b/R/aba.R
@@ -38,7 +38,10 @@
#' observations: not used in the function but exported in the result for use in
#' further inference functions
#' @param threshold vector of length two. minimum and maximum values of threshold
-#' to apply to predicted values
+#' to apply to predicted values. Non-finite values are replaced by the minimum.
+#' Values are replaced after computation of the variance of residuals used for
+#' bias correction
+#' @param ... other parameters to be passed to \code{\link[leaps]{regsubsets}},
#'
#' @seealso \code{\link{aba_combine_strata}} for combining models calibrated
#' on different strata, \code{\link{aba_plot}} for plotting model
@@ -84,7 +87,8 @@ aba_build_model <-
nmax = 3,
test = c("partial_p", "vif", "gvlma"),
xy = NULL,
- threshold = NULL) {
+ threshold = NULL,
+ ...) {
# build data.frame with dependent variable and predictors
df <- data.frame(dep_var = variable, predictors)
row.names(df) <- row.names(predictors)
@@ -147,7 +151,8 @@ aba_build_model <-
nbest = 20,
nvmax = nmax - 1,
method = "exhaustive",
- really.big = TRUE
+ really.big = TRUE,
+ ...
)
)
#-----------------------------------------------------------------------------
@@ -229,6 +234,7 @@ aba_build_model <-
if (!is.null(threshold)) {
prediction <- pmin(prediction, threshold[2])
prediction <- pmax(prediction, threshold[1])
+ prediction[!is.finite(prediction)] <- threshold[1]
}
#
#---------------------------------------------------------------------------
@@ -697,6 +703,7 @@ aba_plot <-
#' \code{log} transformation case
#' @param pkg raster output format. Use pkg = "terra|raster|stars" to get an output in SpatRaster, RasterLayer
#' or stars format.
+#' @param ... other parameters to be passed to \code{\link[stats]{predict.lm}}, e.g. \code{interval = "prediction"},
#' @examples
#' # load data
#' data(quatre_montagnes)
@@ -724,7 +731,8 @@ aba_predict <-
metrics_map,
stratum = NULL,
add_error = FALSE,
- pkg = "terra") {
+ pkg = "terra",
+ ...) {
# convert to terra
if(!inherits(metrics_map, "SpatRaster")) metrics_map <- convert_raster(metrics_map, "terra")
# create factor of stratum if not existing
@@ -757,7 +765,8 @@ aba_predict <-
}
# predict on all cells
r[[stratum_label]] <- terra::predict(newdata,
- model_aba$model[[stratum_label]])
+ model_aba$model[[stratum_label]],
+ ...)
if (model_aba$stats[stratum_label, "transform"] == "boxcox")
# case of Box-Cox transform
diff --git a/R/optical_metrics.R b/R/optical_metrics.R
index ec32722..d704e59 100755
--- a/R/optical_metrics.R
+++ b/R/optical_metrics.R
@@ -7,7 +7,7 @@
#'
#' Computes vegetation indices from the Red, Green and Infra-Red bands of an IRC
#' image and adds them as additional bands or columns. Acronyms are listed on
-#' \url{https://www.l3harrisgeospatial.com/docs/broadbandgreenness.html}. If the
+#' \url{https://www.nv5geospatialsoftware.com/docs/BroadbandGreenness.html}. If the
#' Blue band is also present, additional indices are computed.
#'
#' @param r raster or data.frame. Should contain bands or columns with
diff --git a/README.md b/README.md
index 9e6d2ce..37f14f6 100755
--- a/README.md
+++ b/README.md
@@ -30,8 +30,8 @@ Tutorials using `lidaRtRee` functions are available in the [vignettes](https://f
# Acknowledgements / funding
-`lidaRtRee` development (2018-2021) was funded by the [ADEME](https://www.ademe.fr/en) (french Agency for Ecological Transition) through the [PROTEST](https://protest.inrae.fr/) project (grant 1703C0069 of the GRAINE program).
+`lidaRtRee` development (2018-2021) was funded by the [ADEME](https://www.ademe.fr/en/frontpage/) (french Agency for Ecological Transition) through the [PROTEST](https://protest.inrae.fr/) project (grant 1703C0069 of the GRAINE program).
-[<img src="man/figures/logo-ademe-republique-francaise.jpg" alt="logo-ademe-republique-francaise" width="300"/>](https://www.ademe.fr/en)
+[<img src="man/figures/logo-ademe-republique-francaise.jpg" alt="logo-ademe-republique-francaise" width="300"/>](https://www.ademe.fr/en/frontpage/)
<br>
[<img src="man/figures/logo_inrae.png" alt="logo_inrae" width="330"/>](https://www.inrae.fr/en)
diff --git a/man/aba_build_model.Rd b/man/aba_build_model.Rd
index 363b2c1..c873842 100755
--- a/man/aba_build_model.Rd
+++ b/man/aba_build_model.Rd
@@ -11,7 +11,8 @@ aba_build_model(
nmax = 3,
test = c("partial_p", "vif", "gvlma"),
xy = NULL,
- threshold = NULL
+ threshold = NULL,
+ ...
)
}
\arguments{
@@ -35,7 +36,11 @@ observations: not used in the function but exported in the result for use in
further inference functions}
\item{threshold}{vector of length two. minimum and maximum values of threshold
-to apply to predicted values}
+to apply to predicted values. Non-finite values are replaced by the minimum.
+Values are replaced after computation of the variance of residuals used for
+bias correction}
+
+\item{...}{other parameters to be passed to \code{\link[leaps]{regsubsets}},}
}
\value{
a list with three elements
diff --git a/man/aba_predict.Rd b/man/aba_predict.Rd
index 5d81118..fd9183d 100755
--- a/man/aba_predict.Rd
+++ b/man/aba_predict.Rd
@@ -9,7 +9,8 @@ aba_predict(
metrics_map,
stratum = NULL,
add_error = FALSE,
- pkg = "terra"
+ pkg = "terra",
+ ...
)
}
\arguments{
@@ -29,6 +30,8 @@ N(0, sigma(residuals)) should be added to fitted values; implemented only for
\item{pkg}{raster output format. Use pkg = "terra|raster|stars" to get an output in SpatRaster, RasterLayer
or stars format.}
+
+\item{...}{other parameters to be passed to \code{\link[stats]{predict.lm}}, e.g. \code{interval = "prediction"},}
}
\value{
a raster of predictions obtained by applying the model \code{aba_build_model}
diff --git a/man/add_vegetation_indices.Rd b/man/add_vegetation_indices.Rd
index 54788bf..9caa5c8 100755
--- a/man/add_vegetation_indices.Rd
+++ b/man/add_vegetation_indices.Rd
@@ -21,7 +21,7 @@ a raster or data.frame with added bands or columns
\description{
Computes vegetation indices from the Red, Green and Infra-Red bands of an IRC
image and adds them as additional bands or columns. Acronyms are listed on
-\url{https://www.l3harrisgeospatial.com/docs/broadbandgreenness.html}. If the
+\url{https://www.nv5geospatialsoftware.com/docs/BroadbandGreenness.html}. If the
Blue band is also present, additional indices are computed.
}
\examples{
diff --git a/man/convert_raster.Rd b/man/convert_raster.Rd
index 18a8ec4..a425280 100755
--- a/man/convert_raster.Rd
+++ b/man/convert_raster.Rd
@@ -10,7 +10,7 @@ convert_raster(r, pkg = NULL)
\item{r}{raster object or file name.}
\item{pkg}{package name. Use pkg = "terra|
-raster|stars" to get an output in SpatRaster, RasterLayer or stars format}
+stars" to get an output in SpatRaster or stars format}
}
\value{
A raster object in the specified format
@@ -29,13 +29,6 @@ chm_chablais3 <- terra::rast(chm_chablais3)
# to stars
# chm_stars <- convert_raster(chm_chablais3, pkg = "stars")
# chm_stars
+# convert_raster(chm_stars, pkg = "terra")
# }
-if (require("raster"))
-{
-# to raster
-chm_raster <- convert_raster(chm_chablais3, pkg = "raster")
-chm_raster
-# back to terra
-convert_raster(chm_raster, pkg = "terra")
-}
}
--
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