tdarec (version 0.2.0)

vpd-dials: Tune Vectorizations of Persistent Homology

Description

These tuning functions govern the parameters of vectorizations implemented in TDAvec.

Usage

num_coef(range = c(1L, unknown()), trans = NULL)
poly_type(values = c("R", "S", "T"), trans = NULL)
img_sigma(range = c(unknown(), unknown()), trans = transform_log10())
num_levels(range = c(1L, unknown()), trans = NULL)
weight_func_pl(
  values = c("triangle", "epanechnikov", "tricubic"),
  trans = NULL
)
bandwidth(range = c(unknown(), unknown()), trans = transform_log10())
weight_power(range = c(1, 2), trans = NULL)
num_bars(range = c(1L, unknown()), trans = NULL)
num_bins(range = c(2L, 20L), trans = NULL)
tent_shift(range = c(unknown(), unknown()), trans = transform_log10())

Value

A param object or list of param objects.

Arguments

range

A two-element vector holding the defaults for the smallest and largest possible values, respectively. If a transformation is specified, these values should be in the transformed units.

trans

A trans object from the scales package, such as scales::transform_log10() or scales::transform_reciprocal(). If not provided, the default is used which matches the units used in range. If no transformation, NULL.

values

A character string of possible values.

Details

The parameter num_coef is passed to m in TDAvec::computeComplexPolynomial().

The parameter poly_type is passed to polyType in TDAvec::computeComplexPolynomial().

The parameter img_sigma is passed to sigma in TDAvec::computePersistenceImage().

The parameter num_levels is passed to k in TDAvec::computePersistenceLandscape().

The parameter weight_func_pl is passed to kernel in TDAvec::computePersistenceLandscape().

The parameter bandwidth is passed to h in TDAvec::computePersistenceLandscape().

The parameter weight_power is passed to p in TDAvec::computePersistenceSilhouette().

The parameter num_bars is passed to r in TDAvec::computeTropicalCoordinates().

The parameter num_bins is passed to d in TDAvec::computeTemplateFunction().

The parameter tent_shift is passed to epsilon in TDAvec::computeTemplateFunction().

Examples

data.frame(dist = I(list(eurodist, UScitiesD * 1.6))) %>%
  transform(pd = I(lapply(dist, ripserr::vietoris_rips))) %>%
  subset(select = c(pd)) %>%
  print() -> pd_data

# `num_coef` for `step_vpn_complex_polynomial()`

(nc_man <- num_coef(range = c(1L, 3L)))
grid_regular(nc_man)

# `poly_type` for `step_vpn_complex_polynomial()`

(pt_man <- poly_type(values = c("R", "S")))
grid_regular(pt_man)

# `img_sigma` for `step_vpn_persistence_image()`

(is_man <- img_sigma(range = c(100, 400), trans = NULL))
grid_regular(is_man)

(is_dat <- img_sigma() %>% get_pers_max_frac(x = pd_data))
grid_regular(is_dat)

(is_hom <- img_sigma() %>% get_pers_max_frac(x = pd_data, hom_degrees = seq(2L)))
grid_regular(is_hom)

# `num_levels` for `step_vpn_persistence_landscape()`

(nl_man <- num_levels(range = c(1L, 6L)))
grid_regular(nl_man)

# `weight_func_pl` for `step_vpn_persistence_landscape()`

(wfp_man <- weight_func_pl(values = c("triangle", "tricubic")))
grid_regular(wfp_man)

# `bandwidth` for `step_vpn_persistence_landscape()`

(b_man <- bandwidth(range = c(500, 1500), trans = NULL))
grid_regular(b_man)

(b_dat <- bandwidth() %>% get_pers_max_frac(x = pd_data))
grid_regular(b_dat)

(b_hom <- bandwidth() %>% get_pers_max_frac(x = pd_data, hom_degrees = seq(2L)))
grid_regular(b_hom)

# `weight_power` for `step_vpn_persistence_silhouette()`

(wp_man <- weight_power(range = c(1, 3)))
grid_regular(wp_man)

# `num_bars` for `step_vpn_tropical_coordinates()`

(nb_man <- num_bars(range = c(1L, 3L)))
grid_regular(nb_man)

# `num_bins` for `step_vpn_tent_template_functions()`

(nb_man <- num_bins(range = c(5L, 10L)))
grid_regular(nb_man)

# `tent_shift` for `step_vpn_tent_template_functions()`

(ts_man <- tent_shift(range = c(100, 200), trans = NULL))
grid_regular(ts_man)

(ts_dat <- tent_shift() %>% get_pers_min_mult(x = pd_data))
grid_regular(ts_dat)

(ts_hom <- tent_shift() %>% get_pers_min_mult(x = pd_data, hom_degrees = seq(2L)))
grid_regular(ts_hom)