Given the structure of a formula to be fitted using a data set, the function adds multiple radii
for variables for which the zone of influence (ZOI) or scale of effect (SOE) is to be assessed
through a statistical model. The terms representing the ZOI/SOE variables should be identified
with a pattern (see argument pattern).
It returns the complete formula with all variables and radii for the ZOI/SOE terms.
If predictor_table = TRUE, it also returns a table with information
about each predictor (e.g. whether or not it is a ZOI variable, which radius and shape, to
what type of infrastructure it corresponds), to be used by some of the algorithms
in the penalized regression modeling.
Usage
add_zoi_formula(
f,
zoi_radius,
type = "",
pattern = "XXX",
cumulative = "",
separator = "_",
remove_term = "",
predictor_table = FALSE
)Arguments
- f
[formula]
A formula to be fitted in a statistical model. Here we do not need the actual name of each term, but all ZOI variables whose radius/scale shall be fitted might be added with a pattern, e.g."road_traffic_zoiXXXX". The pattern (e.g"XXXX") needs to be set using the argumentpattern.- zoi_radius
[numeric,vector]
A vector of radii/scales for the zone of influence, to be added to the formula (e.g.c(100, 200, 300)).- type
[character=""]
Shape(s) of the ZOI (or vector of shapes if more than one), to be added to the terms name (e.g."exp","linear").- pattern
[character]
Pattern to be replaced in the formula, corresponding to the ZOI radii or ZOI shapes and radii (e.g."XXX").- cumulative
[character=""]{"cumulative", "nearest"}
Default is"". String to be added to the ZOI terms corresponding on whether the variable represents the ZOI of the nearest feature (cumulative = "nearest") or the cumulative ZOI (cumulative = "cumulative"). If""(default), the type of ZOI is taken from the variable name, already given in the formula.- separator
[character(1)="_"]
Separator to be used between type and zoi_radius, whentypeis provided. Default is"_".- remove_term
[character=""]
Vector of characters with the names of the variables not to be added to the formula. This should be used when some specific combinations of variables, shapes, and radii are in principle created by the function but shouldbe ignored in the final formula.- predictor_table
[logical(1)=FALSE]
logical. Whether or not a table should be returned with info of all ZOI radii, shape values, and formula terms, together with info from other non-ZOI predictors. This table is of special interest when fitting "Decay Adaptive Lasso" or other related models withfit_net_logit()orfit_net_clogit()with argumentmethod = "DecayAdaptiveLasso".
Value
A list with both the final formula with all ZOI radii and shapes and
a table with the predictor information (if predictor_table = TRUE).
Details
The function searches for patterns in ZOI variables as stated in the formula
and replaces them by combinations of strings representing the type of ZOI
(nearest, cumulative), the shape (e.g. "exp", "linear"), and the multiple ZOI radii
to be assessed. The final name of the variables should match the names of the
columns in the data set.
Examples
# multiple radii
f <- case_ ~ strata(step_id_) + sl_*startpt_roadsXXX + sl_*startpt_cabinsXXX
add_zoi_formula(f, zoi_radius = c(1000, 2000, 3000), pattern = "XXX")
#> $formula
#> case_ ~ strata(step_id_) + sl_ * startpt_roads1000 + sl_ * startpt_roads2000 +
#> sl_ * startpt_roads3000 + sl_ * startpt_cabins1000 + sl_ *
#> startpt_cabins2000 + sl_ * startpt_cabins3000
#> <environment: 0x557285318420>
#>
#> $predictor_table
#> [1] FALSE
#>
# multiple radii and shapes
f <- case_ ~ strata(step_id_) + sl_*startpt_roadsXXX + sl_*startpt_cabinsXXX
add_zoi_formula(f, zoi_radius = c(1000, 2000, 3000), type = "_exp_decay", pattern = "XXX")
#> $formula
#> case_ ~ strata(step_id_) + sl_ * startpt_roads_exp_decay_1000 +
#> sl_ * startpt_roads_exp_decay_2000 + sl_ * startpt_roads_exp_decay_3000 +
#> sl_ * startpt_cabins_exp_decay_1000 + sl_ * startpt_cabins_exp_decay_2000 +
#> sl_ * startpt_cabins_exp_decay_3000
#> <environment: 0x5572853f7440>
#>
#> $predictor_table
#> [1] FALSE
#>
add_zoi_formula(f, zoi_radius = c(1000, 2000, 3000), type = c("_exp_decay", "_threshold"), pattern = "XXX")
#> $formula
#> case_ ~ strata(step_id_) + sl_ * startpt_roads_exp_decay_1000 +
#> sl_ * startpt_roads_exp_decay_2000 + sl_ * startpt_roads_exp_decay_3000 +
#> sl_ * startpt_roads_threshold_1000 + sl_ * startpt_roads_threshold_2000 +
#> sl_ * startpt_roads_threshold_3000 + sl_ * startpt_cabins_exp_decay_1000 +
#> sl_ * startpt_cabins_exp_decay_2000 + sl_ * startpt_cabins_exp_decay_3000 +
#> sl_ * startpt_cabins_threshold_1000 + sl_ * startpt_cabins_threshold_2000 +
#> sl_ * startpt_cabins_threshold_3000
#> <environment: 0x557285476208>
#>
#> $predictor_table
#> [1] FALSE
#>
# predictor_table - adding only the nearest ZOI
f <- case_ ~ strata(step_id_) + land_use + sl_*startpt_roads_XXX + sl_*startpt_cabins_XXX
add_zoi_formula(f, zoi_radius = c(1000, 2000, 3000), type = c("exp_decay", "threshold"), pattern = "XXX",
predictor_table = TRUE, cumulative = "nearest")
#> $formula
#> case_ ~ strata(step_id_) + land_use + sl_ * startpt_roads_exp_decay_1000 +
#> sl_ * startpt_roads_exp_decay_2000 + sl_ * startpt_roads_exp_decay_3000 +
#> sl_ * startpt_roads_threshold_1000 + sl_ * startpt_roads_threshold_2000 +
#> sl_ * startpt_roads_threshold_3000 + sl_ * startpt_cabins_exp_decay_1000 +
#> sl_ * startpt_cabins_exp_decay_2000 + sl_ * startpt_cabins_exp_decay_3000 +
#> sl_ * startpt_cabins_threshold_1000 + sl_ * startpt_cabins_threshold_2000 +
#> sl_ * startpt_cabins_threshold_3000
#> <environment: 0x55728552d428>
#>
#> $predictor_table
#> is_zoi cumulative shape zoi_radius variable
#> 1 0 <NA> <NA> NA land_use
#> 7 1 nearest exp_decay 1000 sl_ * startpt_roads_
#> 8 1 nearest exp_decay 2000 sl_ * startpt_roads_
#> 9 1 nearest exp_decay 3000 sl_ * startpt_roads_
#> 10 1 nearest threshold 1000 sl_ * startpt_roads_
#> 11 1 nearest threshold 2000 sl_ * startpt_roads_
#> 12 1 nearest threshold 3000 sl_ * startpt_roads_
#> 13 1 nearest exp_decay 1000 sl_ * startpt_cabins_
#> 14 1 nearest exp_decay 2000 sl_ * startpt_cabins_
#> 15 1 nearest exp_decay 3000 sl_ * startpt_cabins_
#> 16 1 nearest threshold 1000 sl_ * startpt_cabins_
#> 17 1 nearest threshold 2000 sl_ * startpt_cabins_
#> 18 1 nearest threshold 3000 sl_ * startpt_cabins_
#> term_zoi
#> 1 land_use
#> 7 sl_ * startpt_roads_exp_decay_1000
#> 8 sl_ * startpt_roads_exp_decay_2000
#> 9 sl_ * startpt_roads_exp_decay_3000
#> 10 sl_ * startpt_roads_threshold_1000
#> 11 sl_ * startpt_roads_threshold_2000
#> 12 sl_ * startpt_roads_threshold_3000
#> 13 sl_ * startpt_cabins_exp_decay_1000
#> 14 sl_ * startpt_cabins_exp_decay_2000
#> 15 sl_ * startpt_cabins_exp_decay_3000
#> 16 sl_ * startpt_cabins_threshold_1000
#> 17 sl_ * startpt_cabins_threshold_2000
#> 18 sl_ * startpt_cabins_threshold_3000
#>
# predictor_table 2 - adding both nearest and cumulative ZOI
f <- case_ ~ strata(step_id_) + sl_*startpt_roads_cumulative_XXX + sl_*startpt_cabins_nearest_XXX
add_zoi_formula(f, zoi_radius = c(1000, 2000, 3000), type = c("exp_decay", "threshold"), pattern = "XXX",
predictor_table = TRUE)
#> $formula
#> case_ ~ strata(step_id_) + sl_ * startpt_roads_cumulative_exp_decay_1000 +
#> sl_ * startpt_roads_cumulative_exp_decay_2000 + sl_ * startpt_roads_cumulative_exp_decay_3000 +
#> sl_ * startpt_roads_cumulative_threshold_1000 + sl_ * startpt_roads_cumulative_threshold_2000 +
#> sl_ * startpt_roads_cumulative_threshold_3000 + sl_ * startpt_cabins_nearest_exp_decay_1000 +
#> sl_ * startpt_cabins_nearest_exp_decay_2000 + sl_ * startpt_cabins_nearest_exp_decay_3000 +
#> sl_ * startpt_cabins_nearest_threshold_1000 + sl_ * startpt_cabins_nearest_threshold_2000 +
#> sl_ * startpt_cabins_nearest_threshold_3000
#> <environment: 0x5572856bf9d8>
#>
#> $predictor_table
#> is_zoi cumulative shape zoi_radius variable
#> 1 1 cumulative exp_decay 1000 sl_ * startpt_roads_cumulative_
#> 2 1 cumulative exp_decay 2000 sl_ * startpt_roads_cumulative_
#> 3 1 cumulative exp_decay 3000 sl_ * startpt_roads_cumulative_
#> 4 1 cumulative threshold 1000 sl_ * startpt_roads_cumulative_
#> 5 1 cumulative threshold 2000 sl_ * startpt_roads_cumulative_
#> 6 1 cumulative threshold 3000 sl_ * startpt_roads_cumulative_
#> 7 1 nearest exp_decay 1000 sl_ * startpt_cabins_nearest_
#> 8 1 nearest exp_decay 2000 sl_ * startpt_cabins_nearest_
#> 9 1 nearest exp_decay 3000 sl_ * startpt_cabins_nearest_
#> 10 1 nearest threshold 1000 sl_ * startpt_cabins_nearest_
#> 11 1 nearest threshold 2000 sl_ * startpt_cabins_nearest_
#> 12 1 nearest threshold 3000 sl_ * startpt_cabins_nearest_
#> term_zoi
#> 1 sl_ * startpt_roads_cumulative_exp_decay_1000
#> 2 sl_ * startpt_roads_cumulative_exp_decay_2000
#> 3 sl_ * startpt_roads_cumulative_exp_decay_3000
#> 4 sl_ * startpt_roads_cumulative_threshold_1000
#> 5 sl_ * startpt_roads_cumulative_threshold_2000
#> 6 sl_ * startpt_roads_cumulative_threshold_3000
#> 7 sl_ * startpt_cabins_nearest_exp_decay_1000
#> 8 sl_ * startpt_cabins_nearest_exp_decay_2000
#> 9 sl_ * startpt_cabins_nearest_exp_decay_3000
#> 10 sl_ * startpt_cabins_nearest_threshold_1000
#> 11 sl_ * startpt_cabins_nearest_threshold_2000
#> 12 sl_ * startpt_cabins_nearest_threshold_3000
#>
# predictor_table 3 - adding the nearest/cumulative metric within the type argument
f <- case_ ~ strata(step_id_) + sl_*startpt_roads_XXX + sl_*startpt_cabins_XXX
add_zoi_formula(f, zoi_radius = c(1000, 2000, 3000), type = c("nearest_exp_decay", "cumulative_exp_decay"), pattern = "XXX",
predictor_table = TRUE)
#> $formula
#> case_ ~ strata(step_id_) + sl_ * startpt_roads_nearest_exp_decay_1000 +
#> sl_ * startpt_roads_nearest_exp_decay_2000 + sl_ * startpt_roads_nearest_exp_decay_3000 +
#> sl_ * startpt_roads_cumulative_exp_decay_1000 + sl_ * startpt_roads_cumulative_exp_decay_2000 +
#> sl_ * startpt_roads_cumulative_exp_decay_3000 + sl_ * startpt_cabins_nearest_exp_decay_1000 +
#> sl_ * startpt_cabins_nearest_exp_decay_2000 + sl_ * startpt_cabins_nearest_exp_decay_3000 +
#> sl_ * startpt_cabins_cumulative_exp_decay_1000 + sl_ * startpt_cabins_cumulative_exp_decay_2000 +
#> sl_ * startpt_cabins_cumulative_exp_decay_3000
#> <environment: 0x55728582efc0>
#>
#> $predictor_table
#> is_zoi cumulative shape zoi_radius variable
#> 1 1 nearest exp_decay 1000 sl_ * startpt_roads_
#> 2 1 nearest exp_decay 2000 sl_ * startpt_roads_
#> 3 1 nearest exp_decay 3000 sl_ * startpt_roads_
#> 4 1 cumulative exp_decay 1000 sl_ * startpt_roads_
#> 5 1 cumulative exp_decay 2000 sl_ * startpt_roads_
#> 6 1 cumulative exp_decay 3000 sl_ * startpt_roads_
#> 7 1 nearest exp_decay 1000 sl_ * startpt_cabins_
#> 8 1 nearest exp_decay 2000 sl_ * startpt_cabins_
#> 9 1 nearest exp_decay 3000 sl_ * startpt_cabins_
#> 10 1 cumulative exp_decay 1000 sl_ * startpt_cabins_
#> 11 1 cumulative exp_decay 2000 sl_ * startpt_cabins_
#> 12 1 cumulative exp_decay 3000 sl_ * startpt_cabins_
#> term_zoi
#> 1 sl_ * startpt_roads_nearest_exp_decay_1000
#> 2 sl_ * startpt_roads_nearest_exp_decay_2000
#> 3 sl_ * startpt_roads_nearest_exp_decay_3000
#> 4 sl_ * startpt_roads_cumulative_exp_decay_1000
#> 5 sl_ * startpt_roads_cumulative_exp_decay_2000
#> 6 sl_ * startpt_roads_cumulative_exp_decay_3000
#> 7 sl_ * startpt_cabins_nearest_exp_decay_1000
#> 8 sl_ * startpt_cabins_nearest_exp_decay_2000
#> 9 sl_ * startpt_cabins_nearest_exp_decay_3000
#> 10 sl_ * startpt_cabins_cumulative_exp_decay_1000
#> 11 sl_ * startpt_cabins_cumulative_exp_decay_2000
#> 12 sl_ * startpt_cabins_cumulative_exp_decay_3000
#>