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fix accessors
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@VLucet
VLucet committed Jan 25, 2022
1 parent f4fdf3a commit 555c88e
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Showing 9 changed files with 164 additions and 24 deletions.
12 changes: 12 additions & 0 deletions NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -9,12 +9,14 @@ export("is_mapped<-")
export("is_split<-")
export("method_func<-")
export("raw_formula<-")
export("spm_biomass_vars<-")
export("spm_boundaries<-")
export("spm_boundary<-")
export("spm_boundary_area<-")
export("spm_coords_col<-")
export("spm_data<-")
export("spm_datasets<-")
export("spm_density_vars<-")
export("spm_discret_method<-")
export("spm_formulas<-")
export("spm_get_fit<-")
Expand All @@ -25,6 +27,7 @@ export("spm_points<-")
export("spm_response<-")
export("spm_smoothed_data<-")
export("spm_smoothed_fit<-")
export("spm_smoothed_vars<-")
export("spm_time<-")
export("spm_unique_ID<-")
export("translated_formula<-")
Expand All @@ -48,12 +51,14 @@ export(spm_aggregate)
export(spm_aggregate_catch)
export(spm_as_boundary)
export(spm_as_dataset)
export(spm_biomass_vars)
export(spm_boundaries)
export(spm_boundary)
export(spm_boundary_area)
export(spm_coords_col)
export(spm_data)
export(spm_datasets)
export(spm_density_vars)
export(spm_discret_method)
export(spm_discretize)
export(spm_formulas)
Expand All @@ -69,6 +74,7 @@ export(spm_smooth)
export(spm_smooth_methods)
export(spm_smoothed_data)
export(spm_smoothed_fit)
export(spm_smoothed_vars)
export(spm_split)
export(spm_time)
export(spm_unique_ID)
Expand All @@ -85,12 +91,14 @@ exportMethods("is_mapped<-")
exportMethods("is_split<-")
exportMethods("method_func<-")
exportMethods("raw_formula<-")
exportMethods("spm_biomass_vars<-")
exportMethods("spm_boundaries<-")
exportMethods("spm_boundary<-")
exportMethods("spm_boundary_area<-")
exportMethods("spm_coords_col<-")
exportMethods("spm_data<-")
exportMethods("spm_datasets<-")
exportMethods("spm_density_vars<-")
exportMethods("spm_discret_method<-")
exportMethods("spm_formulas<-")
exportMethods("spm_get_fit<-")
Expand All @@ -101,6 +109,7 @@ exportMethods("spm_points<-")
exportMethods("spm_response<-")
exportMethods("spm_smoothed_data<-")
exportMethods("spm_smoothed_fit<-")
exportMethods("spm_smoothed_vars<-")
exportMethods("spm_time<-")
exportMethods("spm_unique_ID<-")
exportMethods("translated_formula<-")
Expand All @@ -123,12 +132,14 @@ exportMethods(spm_aggregate)
exportMethods(spm_aggregate_catch)
exportMethods(spm_as_boundary)
exportMethods(spm_as_dataset)
exportMethods(spm_biomass_vars)
exportMethods(spm_boundaries)
exportMethods(spm_boundary)
exportMethods(spm_boundary_area)
exportMethods(spm_coords_col)
exportMethods(spm_data)
exportMethods(spm_datasets)
exportMethods(spm_density_vars)
exportMethods(spm_discret_method)
exportMethods(spm_discretize)
exportMethods(spm_formulas)
Expand All @@ -142,6 +153,7 @@ exportMethods(spm_response)
exportMethods(spm_smooth)
exportMethods(spm_smoothed_data)
exportMethods(spm_smoothed_fit)
exportMethods(spm_smoothed_vars)
exportMethods(spm_split)
exportMethods(spm_time)
exportMethods(spm_unique_ID)
Expand Down
105 changes: 105 additions & 0 deletions R/accessors-methods-sspm_dataset.R
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Original file line number Diff line number Diff line change
Expand Up @@ -145,6 +145,76 @@ setMethod("spm_time<-",
}
)

# Biomass -----------------------------------------------------------------
# Accessors ---------------------------------------------------------------

#' @rdname accessors-methods-sspm_dataset
#' @export
setGeneric(name = "spm_biomass_vars",
def = function(sspm_object) standardGeneric("spm_biomass_vars")
)

#' @rdname accessors-methods-sspm_dataset
#' @export
setMethod("spm_biomass_vars",
signature("sspm_object" = "sspm_dataset"),
function(sspm_object) sspm_object@biomass
)

# Replacers ---------------------------------------------------------------

#' @rdname accessors-methods-sspm_dataset
#' @export
setGeneric(name = "spm_biomass_vars<-",
def = function(object, value) standardGeneric("spm_biomass_vars<-")
)

#' @rdname accessors-methods-sspm_dataset
#' @export
setMethod("spm_biomass_vars<-",
signature("object" = "sspm_dataset"),
function(object, value) {
object@biomass <- value
validObject(object)
return(object)
}
)

# Biomass -----------------------------------------------------------------
# Accessors ---------------------------------------------------------------

#' @rdname accessors-methods-sspm_dataset
#' @export
setGeneric(name = "spm_density_vars",
def = function(sspm_object) standardGeneric("spm_density_vars")
)

#' @rdname accessors-methods-sspm_dataset
#' @export
setMethod("spm_density_vars",
signature("sspm_object" = "sspm_dataset"),
function(sspm_object) sspm_object@density
)

# Replacers ---------------------------------------------------------------

#' @rdname accessors-methods-sspm_dataset
#' @export
setGeneric(name = "spm_density_vars<-",
def = function(object, value) standardGeneric("spm_density_vars<-")
)

#' @rdname accessors-methods-sspm_dataset
#' @export
setMethod("spm_density_vars<-",
signature("object" = "sspm_dataset"),
function(object, value) {
object@density <- value
validObject(object)
return(object)
}
)

# Formulas ----------------------------------------------------------------
# Accessors ---------------------------------------------------------------

Expand Down Expand Up @@ -238,6 +308,41 @@ setMethod("spm_smoothed_fit<-",
}
)

# Smoothed var ------------------------------------------------------------
# Accessors ---------------------------------------------------------------

#' @rdname accessors-methods-sspm_dataset
#' @export
setGeneric(name = "spm_smoothed_vars",
def = function(sspm_object) standardGeneric("spm_smoothed_vars")
)

#' @rdname accessors-methods-sspm_dataset
#' @export
setMethod("spm_smoothed_vars",
signature("sspm_object" = "sspm_dataset"),
function(sspm_object) sspm_object@smoothed_vars
)

# Replacers ---------------------------------------------------------------

#' @rdname accessors-methods-sspm_dataset
#' @export
setGeneric(name = "spm_smoothed_vars<-",
def = function(object, value) standardGeneric("spm_smoothed_vars<-")
)

#' @rdname accessors-methods-sspm_dataset
#' @export
setMethod("spm_smoothed_vars<-",
signature("object" = "sspm_dataset"),
function(object, value) {
object@smoothed_vars <- value
validObject(object)
return(object)
}
)

# Is mapped ---------------------------------------------------------------
# Accessors ---------------------------------------------------------------

Expand Down
4 changes: 2 additions & 2 deletions R/fit.R
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Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@ setMethod(f = "fit_smooths",
patches <- spm_patches(boundaries)

# Initialize/collect smoothed_vars/fit
full_smoothed_vars <- sspm_object@smoothed_vars
full_smoothed_vars <- spm_smoothed_vars(sspm_object)
if (is.null(full_smoothed_vars)) {
full_smoothed_vars <- c()
}
Expand Down Expand Up @@ -130,7 +130,7 @@ setMethod(f = "fit_smooths",
}

full_smoothed_vars <- c(full_smoothed_vars, response)
sspm_object@smoothed_vars <- full_smoothed_vars
spm_smoothed_vars(sspm_object) <- full_smoothed_vars

return(sspm_object)
}
Expand Down
4 changes: 2 additions & 2 deletions R/plot.R
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Original file line number Diff line number Diff line change
Expand Up @@ -47,8 +47,8 @@ setMethod("plot",

if (checkmate::test_class(x, "sspm_discrete_boundary")) {

patches <- x@patches
points <- x@points
patches <- spm_patches(x)
points <- spm_points(x)

sspm_discrete_plot <- ggplot2::ggplot() +
ggplot2::geom_sf(data = patches,
Expand Down
4 changes: 2 additions & 2 deletions R/predict.R
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Original file line number Diff line number Diff line change
Expand Up @@ -241,8 +241,8 @@ setMethod(f = "predict",
type = type))
names(preds) <- responses

biomass_vars <- c(object@biomass)
biomass_density_vars <- c(object@density)
biomass_vars <- c(spm_biomass_vars(object))
biomass_density_vars <- c(spm_density_vars(object))

for (var in names(preds)){
if (var %in% biomass_vars){
Expand Down
2 changes: 1 addition & 1 deletion R/spm_discretize.R
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Original file line number Diff line number Diff line change
Expand Up @@ -138,7 +138,7 @@ setMethod(f = "spm_discretize",
cli::col_yellow(spm_name(method))))

# Send to discretization routine
boundaries <- boundary_object@boundaries
boundaries <- spm_boundaries(boundary_object)
boundary <- spm_boundary(boundary_object)
other_args <- list(...)

Expand Down
2 changes: 1 addition & 1 deletion R/spm_smooth.R
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Original file line number Diff line number Diff line change
Expand Up @@ -140,7 +140,7 @@ join_datasets <- function(sspm_dataset, sspm_boundary) {
checkmate::assert_class(sspm_boundary, "sspm_discrete_boundary")

the_data <- spm_data(sspm_dataset)
the_patches <- sspm_boundary@patches
the_patches <- spm_patches(sspm_boundary)

# TODO REVIEW THE COHERENCE OF ST_TRANSFORM
joined <- suppressMessages(sf::st_transform(the_data, crs = sf::st_crs(the_patches)))
Expand Down
19 changes: 3 additions & 16 deletions R/sspm.R
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Original file line number Diff line number Diff line change
Expand Up @@ -29,20 +29,13 @@ setMethod(f = "sspm",
predictors = "missing"),
function(biomass, predictors) {

# if (!checkmate::test_subset(biomass_var,
# names(spm_data(biomass)))) {
# stop("`biomass_var` must be a column of `biomass`",
# call. = FALSE)
# }

new_sspm <- new("sspm",
datasets = list(biomass = biomass),
time = spm_time(biomass),
# biomass_var = biomass_var,
uniqueID = "row_ID",
boundaries = spm_boundaries(biomass),
smoothed_data = spm_smoothed_data(biomass),
smoothed_vars = biomass@smoothed_vars,
smoothed_vars = spm_smoothed_vars(biomass),
is_split = FALSE)

}
Expand Down Expand Up @@ -85,12 +78,6 @@ setMethod(f = "sspm",
predictors_boundaries))
check_identical_boundaries(all_boundaries)

# if (!checkmate::test_subset(biomass_var,
# names(spm_data(biomass)))) {
# stop("`biomass_var` must be a column of `biomass`",
# call. = FALSE)
# }

# 3. combine the full_smoothed_data/vars
# TODO message about catch
info_message <-
Expand All @@ -105,7 +92,7 @@ setMethod(f = "sspm",
}

full_smoothed_data <- biomass_clean
full_smoothed_vars <- biomass@smoothed_vars
full_smoothed_vars <- spm_smoothed_vars(biomass)

for (predictor in predictors) {

Expand All @@ -124,7 +111,7 @@ setMethod(f = "sspm",
spm_time(biomass)),
suffix = the_suffix)

predictor_smoothed_vars <- predictor@smoothed_vars
predictor_smoothed_vars <- spm_smoothed_vars(predictor)

# Check same vars
same_vars <-
Expand Down
36 changes: 36 additions & 0 deletions man/accessors-methods-sspm_dataset.Rd
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