Nothing
## Style UI choices ------------------------------------------------------------
#' Combined string of mineral names and their formulas for UI choosing focal from minerals
#' @noRd
mineral_names_formulas <- function(med_data = med_data_cache){
med_data %>%
dplyr::select(mineral_name, ima_chemistry) %>%
dplyr::distinct() %>%
dplyr::arrange(mineral_name) %>%
dplyr::mutate(both = paste0(mineral_name, " (", ima_chemistry, ")")) %>%
dplyr::pull(both)
}
#' UI options for selecting a color scheme for minerals in the TIMELINE
#' @noRd
mineral_timeline_color_by_choices <- setNames(c("singlecolor",
"w_mean_pauling",
"mean_pauling",
"w_cov_pauling",
"cov_pauling",
"num_localities",
"max_age"),
c(singlecolor_str,
w_mean_pauling_str,
mean_pauling_str,
w_cov_pauling_str,
cov_pauling_str,
num_localities_str,
max_age_str))
#' UI options for selecting a variable to color element nodes by
#' @noRd
element_color_by_choices <- setNames(c("singlecolor",
"network_degree_norm",
"pauling",
"element_redox_network",
"element_hsab",
"num_localities",
"atomic_mass",
"element_density",
"element_specific_heat",
"element_crust_percent_weight"),
c(singlecolor_str,
network_degree_norm_str,
pauling_str,
element_redox_network_str,
element_hsab_str,
num_localities_element_str,
atomic_mass_str,
element_density_str,
element_specific_heat_str,
element_crust_percent_weight_str))
#' UI options for selecting a variable to color mineral nodes by
#' @noRd
mineral_color_by_choices <- setNames(c("singlecolor",
"max_age",
"num_localities",
"w_mean_pauling",
"mean_pauling",
"w_cov_pauling",
"cov_pauling"),
c(singlecolor_str,
max_age_str,
num_localities_mineral_str,
w_mean_pauling_str,
mean_pauling_str,
w_cov_pauling_str,
cov_pauling_str))
#' UI options for selecting a variable to size element nodes by
#' @noRd
element_size_by_choices <- setNames(c("singlesize",
"network_degree_norm",
"closeness",
"num_localities"),
c(singlesize_str,
network_degree_norm_str,
closeness_str,
num_localities_element_str))
#' UI options for selecting a variable to size mineral nodes by
#' @noRd
mineral_size_by_choices <- setNames(c("singlesize",
"max_age",
"num_localities"),
c(singlesize_str,
max_age_str,
num_localities_mineral_str))
#' UI options for selecting a variable to color network edges by
#' @noRd
edge_color_by_choices <- setNames(c("singlecolor",
"max_age",
"w_mean_pauling",
"mean_pauling",
"w_cov_pauling",
"cov_pauling",
"element_redox_network",
"element_redox_mineral",
"num_localities_mineral"),
c(singlecolor_str,
max_age_str,
w_mean_pauling_str,
mean_pauling_str,
w_cov_pauling_str,
cov_pauling_str,
element_redox_network_str,
element_redox_mineral_str,
num_localities_mineral_str))
#' UI options for selecting an element node shape
#' @noRd
element_shape_choices <- c("Circle" = "circle",
"Square" = "box",
"Text only (no shape)" = "text")
#' UI options for selecting a mineral node shape
#' @noRd
mineral_shape_choices <- c("Circle" = "dot", #### !!!!!!
"Square" = "square")
## Modeling choices ----------------------------------------
#' UI options for response variables to use in linear model
#' @noRd
model_response_choices <- c(max_age_str,
w_mean_pauling_str,
mean_pauling_str,
w_cov_pauling_str,
cov_pauling_str,
network_degree_norm_str,
closeness_str,
num_localities_str)
#' UI options for predictor variables to use in linear model
#' @noRd
model_predictor_choices <- c(model_response_choices, cluster_ID_str)
#' List of which variables that can be used in linear models are categorical
#' @noRd
categorical_model_variables <- c(cluster_ID_str)
#' UI options for type of plot to display when building a model with a categorical predictor variable
#' @noRd
categorical_plot_choices <- c("Strip chart" = "strip",
"Violin plot" = "violin",
"Sina plot" = "sina",
"Boxplot" = "boxplot")
## Network construction choices -----------------------------------------------------------
#' UI options for network layout
#' @noRd
network_layout_choices <- list(`Force-directed` = c("Fruchterman Reingold" = "layout_with_fr",
"GEM force-directed" = "layout_with_gem"),
Other = c("Dynamic physics layout" = "physics",
"Sugiyama (bipartite) Layout" = "layout_with_sugiyama",
"Layout in circle" = "layout_in_circle",
"Layout in sphere" = "layout_on_sphere"))
#' UI options for specifically physics (non-static) network layouts
#' @noRd
physics_choices <- c("forceAtlas2Based" = "forceAtlas2Based",
"Barnes-Hut" = "barnesHut",
"Repulsion" = "repulsion",
"Hierarchical repulsion" = "hierarchicalRepulsion")
#' UI options for community clustering algorithms
#' @noRd
cluster_algorithm_choices <- c(cluster_alg_louvain_str, cluster_alg_eig_str)
## Arrays used in selected_node_table drop-down menus --------------------------------------------------
#' Variables to always appear in selected node table
#' @noRd
selected_node_table_constant <- c(element_str, mineral_name_str)
#' Variables choices for mineral attributes to appear in the selected node table
#' @noRd
selected_node_table_column_choices_mineral <- c(mineral_id_str,
rruff_chemistry_str,
ima_chemistry_str,
max_age_str,
num_localities_mineral_str,
w_mean_pauling_str,
mean_pauling_str,
w_cov_pauling_str,
cov_pauling_str)
## NOT CURRENTLY USED
# Variables choices for mineral locality attributes to appear in the selected node table
# @noRd
#selected_node_table_column_choices_locality <- c(mindat_id_str,
# locality_longname_str,
# age_type_str,
# max_age_locality_str,
# min_age_locality_str)
#' Variables choices for element attributes to appear in the selected node table
#' @noRd
selected_node_table_column_choices_element <- c(pauling_str,
element_redox_network_str,
element_redox_mineral_str,
element_hsab_str,
element_metal_type_str,
element_crust_percent_weight_str)
## BOTH ELEMENT AND MINERAL COLUMNS HAVE TO APPEAR WHEN SELECTED
#' Variables choices for network-level node attributes to appear in the selected node table
#' @noRd
selected_node_table_column_choices_network <- c(cluster_ID_str,
closeness_str,
network_degree_norm_str)
#' List of choices for how igraph can format the output network
#' @noRd
igraph_output_format_choices <- c("GraphML" = "graphml",
"GML (Graph Modeling Language)" = "gml",
"DOT" = "dot",
"Pajek" = "pajek",
"ncol" = "ncol",
"Large Graph Layout (LGL)" = "lgl",
"LEDA" = "leda",
"Edge list" = "edgelist")
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