diff --git a/DESCRIPTION b/DESCRIPTION index 09771901..923a71cf 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: rgeoda Type: Package Title: R Library for Spatial Data Analysis -Version: 0.0.10-4 -Date: 2023-07-01 +Version: 0.0.11-1 +Date: 2024-12-18 Authors@R: c(person(given = "Xun", family = "Li", email="lixun910@gmail.com", role=c("aut","cre")), person(given = "Luc", family = "Anselin", email="anselin@uchicago.edu", role="aut")) @@ -33,8 +33,8 @@ Imports: Rcpp (>= 1.0.1) LinkingTo: Rcpp, - BH -RoxygenNote: 7.1.1 + BH (>= 1.87.0-1) +RoxygenNote: 7.3.2 Encoding: UTF-8 Suggests: wkb, diff --git a/NAMESPACE b/NAMESPACE index 878a1987..5058f683 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -59,6 +59,10 @@ export(min_distthreshold) export(min_neighbors) export(natural_breaks) export(neighbor_match_test) +export(p_GeoDa) +export(p_GeoDaTable) +export(p_GeoDaWeight) +export(p_LISA) export(percentile_breaks) export(quantile_breaks) export(queen_weights) diff --git a/R/clustering.R b/R/clustering.R index 8f82a405..c597bd91 100644 --- a/R/clustering.R +++ b/R/clustering.R @@ -9,8 +9,8 @@ #' @param bound_variable (optional) A data frame with selected bound variable #' @param min_bound (optional) A minimum bound value that applies to all #' clusters -#' @param scale_method One of the scaling methods {'raw', 'standardize', -#' 'demean', 'mad', 'range_standardize', 'range_adjust'} to apply on input data. +#' @param scale_method One of the scaling methods ('raw', 'standardize', +#' 'demean', 'mad', 'range_standardize', 'range_adjust') to apply on input data. #' Default is 'standardize' (Z-score normalization). #' @param distance_method (optional) The distance method used to compute the #' distance betwen observation i and j. Defaults to "euclidean". Options are @@ -89,7 +89,7 @@ skater <- function(k, w, df, bound_variable=data.frame(), min_bound=0, #' @param method {"single", "complete", "average","ward"} #' @param bound_variable (optional) A data frame with selected bound variabl #' @param min_bound (optional) A minimum bound value that applies to all clusters -#' @param scale_method One of the scaling methods {'raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust'} to apply on input data. Default is 'standardize' (Z-score normalization). +#' @param scale_method One of the scaling methods ('raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust') to apply on input data. Default is 'standardize' (Z-score normalization). #' @param distance_method (optional) The distance method used to compute the distance betwen observation i and j. Defaults to "euclidean". Options are "euclidean" and "manhattan" #' @param rdist (optional) The distance matrix (lower triangular matrix, column wise storage) #' @return A names list with names "Clusters", "Total sum of squares", "Within-cluster sum of squares", "Total within-cluster sum of squares", and "The ratio of between to total sum of squares". @@ -125,7 +125,7 @@ schc <- function(k, w, df, method="average", bound_variable=data.frame(), min_bo scale_methods <- c('raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust') if (!(scale_method %in% scale_methods)) { - stop("The scale_method has to be one of {'raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust'}") + stop("The scale_method has to be one of ('raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust')") } method_cands <- c("single", "complete", "average","ward") @@ -166,7 +166,7 @@ schc <- function(k, w, df, method="average", bound_variable=data.frame(), min_bo #' @param method {"firstorder-singlelinkage", "fullorder-completelinkage", "fullorder-averagelinkage","fullorder-singlelinkage", "fullorder-wardlinkage"} #' @param bound_variable (optional) A data frame with selected bound variabl #' @param min_bound (optional) A minimum bound value that applies to all clusters -#' @param scale_method (optional) One of the scaling methods {'raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust'} to apply on input data. Default is 'standardize' (Z-score normalization). +#' @param scale_method (optional) One of the scaling methods ('raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust') to apply on input data. Default is 'standardize' (Z-score normalization). #' @param distance_method (optional) The distance method used to compute the distance betwen observation i and j. Defaults to "euclidean". Options are "euclidean" and "manhattan" #' @param random_seed (int,optional) The seed for random number generator. Defaults to 123456789. #' @param cpu_threads (optional) The number of cpu threads used for parallel computation @@ -238,7 +238,7 @@ redcap <- function(k, w, df, method="fullorder-averagelinkage", bound_variable=d #' @param min_bound A minimum value that the sum value of bounding variable int each cluster should be greater than #' @param iterations (optional): The number of iterations of greedy algorithm. Defaults to 99. #' @param initial_regions (optional): The initial regions that the local search starts with. Default is empty. means the local search starts with a random process to "grow" clusters -#' @param scale_method (optional) One of the scaling methods {'raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust'} to apply on input data. Default is 'standardize' (Z-score normalization). +#' @param scale_method (optional) One of the scaling methods ('raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust') to apply on input data. Default is 'standardize' (Z-score normalization). #' @param distance_method (optional) The distance method used to compute the distance betwen observation i and j. Defaults to "euclidean". Options are "euclidean" and "manhattan" #' @param random_seed (optional) The seed for random number generator. Defaults to 123456789. #' @param cpu_threads (optional) The number of cpu threads used for parallel computation @@ -313,7 +313,7 @@ maxp_greedy <- function(w, df, bound_variable, min_bound, iterations=99, initial #' @param cooling_rate The cooling rate of a simulated annealing algorithm. Defaults to 0.85 #' @param iterations (optional): The number of iterations of SA algorithm. Defaults to 99. #' @param sa_maxit (optional): The number of iterations of simulated annealing. Defaults to 1 -#' @param scale_method (optional) One of the scaling methods {'raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust'} to apply on input data. Default is 'standardize' (Z-score normalization). +#' @param scale_method (optional) One of the scaling methods ('raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust') to apply on input data. Default is 'standardize' (Z-score normalization). #' @param distance_method (optional) The distance method used to compute the distance betwen observation i and j. Defaults to "euclidean". Options are "euclidean" and "manhattan" #' @param random_seed (optional) The seed for random number generator. Defaults to 123456789. #' @param initial_regions (optional): The initial regions that the local search starts with. Default is empty. means the local search starts with a random process to "grow" clusters @@ -389,7 +389,7 @@ maxp_sa <- function(w, df, bound_variable, min_bound, cooling_rate, sa_maxit=1, #' @param tabu_length (optional): The length of a tabu search heuristic of tabu algorithm. Defaults to 10. #' @param conv_tabu (optional): The number of non-improving moves. Defaults to 10. #' @param iterations (optional): The number of iterations of Tabu algorithm. Defaults to 99. -#' @param scale_method (optional) One of the scaling methods {'raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust'} to apply on input data. Default is 'standardize' (Z-score normalization). +#' @param scale_method (optional) One of the scaling methods ('raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust') to apply on input data. Default is 'standardize' (Z-score normalization). #' @param distance_method (optional) The distance method used to compute the distance betwen observation i and j. Defaults to "euclidean". Options are "euclidean" and "manhattan" #' @param random_seed (optional) The seed for random number generator. Defaults to 123456789. #' @param initial_regions (optional): The initial regions that the local search starts with. Default is empty. means the local search starts with a random process to "grow" clusters @@ -462,7 +462,7 @@ maxp_tabu <- function(w, df, bound_variable, min_bound, tabu_length=10, conv_tab #' @param min_bound (optional) A minimum bound value that applies to all clusters #' @param inits (optional) The number of construction re-runs, which is for ARiSeL "automatic regionalization with initial seed location" #' @param initial_regions (optional) The initial regions that the local search starts with. Default is empty. means the local search starts with a random process to "grow" clusters -#' @param scale_method (optional) One of the scaling methods {'raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust'} to apply on input data. Default is 'standardize' (Z-score normalization). +#' @param scale_method (optional) One of the scaling methods ('raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust') to apply on input data. Default is 'standardize' (Z-score normalization). #' @param distance_method (optional) The distance method used to compute the distance betwen observation i and j. Defaults to "euclidean". Options are "euclidean" and "manhattan" #' @param random_seed (optional) The seed for random number generator. Defaults to 123456789. #' @param rdist (optional) The distance matrix (lower triangular matrix, column wise storage) @@ -528,7 +528,7 @@ azp_greedy <- function(p, w, df, bound_variable=data.frame(), min_bound=0, inits #' @param min_bound (optional) A minimum bound value that applies to all clusters #' @param inits (optional) The number of construction re-runs, which is for ARiSeL "automatic regionalization with initial seed location" #' @param initial_regions (optional) The initial regions that the local search starts with. Default is empty. means the local search starts with a random process to "grow" clusters -#' @param scale_method (optional) One of the scaling methods {'raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust'} to apply on input data. Default is 'standardize' (Z-score normalization). +#' @param scale_method (optional) One of the scaling methods ('raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust') to apply on input data. Default is 'standardize' (Z-score normalization). #' @param distance_method (optional) The distance method used to compute the distance betwen observation i and j. Defaults to "euclidean". Options are "euclidean" and "manhattan" #' @param random_seed (optional) The seed for random number generator. Defaults to 123456789. #' @param rdist (optional) The distance matrix (lower triangular matrix, column wise storage) @@ -594,7 +594,7 @@ azp_sa<- function(p, w, df, cooling_rate, sa_maxit=1, bound_variable=data.frame( #' @param min_bound (optional) A minimum bound value that applies to all clusters #' @param inits (optional) The number of construction re-runs, which is for ARiSeL "automatic regionalization with initial seed location" #' @param initial_regions (optional) The initial regions that the local search starts with. Default is empty. means the local search starts with a random process to "grow" clusters -#' @param scale_method (optional) One of the scaling methods {'raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust'} to apply on input data. Default is 'standardize' (Z-score normalization). +#' @param scale_method (optional) One of the scaling methods ('raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust') to apply on input data. Default is 'standardize' (Z-score normalization). #' @param distance_method (optional) The distance method used to compute the distance betwen observation i and j. Defaults to "euclidean". Options are "euclidean" and "manhattan" #' @param random_seed (optional) The seed for random number generator. Defaults to 123456789. #' @param rdist (optional) The distance matrix (lower triangular matrix, column wise storage) diff --git a/R/lisa.R b/R/lisa.R index b21db10b..32ff5f67 100644 --- a/R/lisa.R +++ b/R/lisa.R @@ -282,7 +282,7 @@ lisa_colors <- function(gda_lisa) { #' @param permutations (optional) The number of permutations for the LISA #' computation #' @param permutation_method (optional) The permutation method used for the -#' LISA computation. Options are {'complete', 'lookup'}. Default is 'complete'. +#' LISA computation. Options are ('complete', 'lookup'). Default is 'complete'. #' @param significance_cutoff (optional) A cutoff value for significance #' p-values to filter not-significant clusters #' @param cpu_threads (optional) The number of cpu threads used for parallel @@ -324,7 +324,7 @@ local_moran <- function(w, df, permutations=999, permutation_method="complete", #' @param permutations (optional) The number of permutations for the LISA #' computation #' @param permutation_method (optional) The permutation method used for the -#' LISA computation. Options are {'complete', 'lookup'}. Default is 'complete'. +#' LISA computation. Options are ('complete', 'lookup'). Default is 'complete'. #' @param significance_cutoff (optional) A cutoff value for significance #' p-values to filter not-significant clusters #' @param cpu_threads (optional) The number of cpu threads used for parallel @@ -381,7 +381,7 @@ local_bimoran <- function(w, df, permutations=999, permutation_method="complete" #' @param permutations (optional) The number of permutations for the LISA #' computation #' @param permutation_method (optional) The permutation method used for the LISA -#' computation. Options are {'complete', 'lookup'}. Default is 'complete'. +#' computation. Options are ('complete', 'lookup'). Default is 'complete'. #' @param significance_cutoff (optional) A cutoff value for significance #' p-values to filter not-significant clusters #' @param cpu_threads (optional) The number of cpu threads used for parallel @@ -430,7 +430,7 @@ local_moran_eb <- function(w, df, permutations=999, #' @param permutations (optional) The number of permutations for the LISA #' computation #' @param permutation_method (optional) The permutation method used for the -#' LISA computation. Options are {'complete', 'lookup'}. Default is 'complete'. +#' LISA computation. Options are ('complete', 'lookup'). Default is 'complete'. #' @param significance_cutoff (optional) A cutoff value for significance #' p-values to filter not-significant clusters #' @param cpu_threads (optional) The number of cpu threads used for parallel @@ -473,7 +473,7 @@ local_geary <- function(w, df, permutations=999, permutation_method="complete", #' @param permutations (optional) The number of permutations for the LISA #' computation #' @param permutation_method (optional) The permutation method used for the -#' LISA computation. Options are {'complete', 'lookup'}. Default is 'complete'. +#' LISA computation. Options are ('complete', 'lookup'). Default is 'complete'. #' @param significance_cutoff (optional) A cutoff value for significance #' p-values to filter not-significant clusters #' @param cpu_threads (optional) The number of cpu threads used for parallel @@ -523,7 +523,7 @@ local_multigeary <- function(w, df, permutations=999, #' @param permutations (optional) The number of permutations for the LISA #' computation #' @param permutation_method (optional) The permutation method used for the -#' LISA computation. Options are {'complete', 'lookup'}. Default is 'complete'. +#' LISA computation. Options are ('complete', 'lookup'). Default is 'complete'. #' @param significance_cutoff (optional) A cutoff value for significance #' p-values to filter not-significant clusters #' @param cpu_threads (optional) The number of cpu threads used for parallel @@ -563,7 +563,7 @@ local_g <- function(w, df, permutations=999, permutation_method="complete", #' @param permutations (optional) The number of permutations for the LISA #' computation #' @param permutation_method (optional) The permutation method used for the -#' LISA computation. Options are {'complete', 'lookup'}. Default is 'complete'. +#' LISA computation. Options are ('complete', 'lookup'). Default is 'complete'. #' @param significance_cutoff (optional) A cutoff value for significance #' p-values to filter not-significant clusters #' @param cpu_threads (optional) The number of cpu threads used for parallel @@ -605,7 +605,7 @@ local_gstar <- function(w, df, permutations=999, permutation_method="complete", #' @param permutations (optional) The number of permutations for the LISA #' computation #' @param permutation_method (optional) The permutation method used for the -#' LISA computation. Options are {'complete', 'lookup'}. Default is 'complete'. +#' LISA computation. Options are ('complete', 'lookup'). Default is 'complete'. #' @param significance_cutoff (optional) A cutoff value for significance #' p-values to filter not-significant clusters #' @param cpu_threads (optional) The number of cpu threads used for parallel @@ -659,7 +659,7 @@ local_joincount <- function(w, df, permutations=999, #' @param permutations (optional) The number of permutations for the LISA #' computation #' @param permutation_method (optional) The permutation method used for the -#' LISA computation. Options are {'complete', 'lookup'}. Default is 'complete'. +#' LISA computation. Options are ('complete', 'lookup'). Default is 'complete'. #' @param significance_cutoff (optional) A cutoff value for significance #' p-values to filter not-significant clusters #' @param cpu_threads (optional) The number of cpu threads used for parallel @@ -724,7 +724,7 @@ local_bijoincount <- function(w, df, permutations=999, #' @param permutations (optional) The number of permutations for the LISA #' computation #' @param permutation_method (optional) The permutation method used for the -#' LISA computation. Options are {'complete', 'lookup'}. Default is 'complete'. +#' LISA computation. Options are ('complete', 'lookup'). Default is 'complete'. #' @param significance_cutoff (optional) A cutoff value for significance #' p-values to filter not-significant clusters #' @param cpu_threads (optional) The number of cpu threads used for parallel @@ -798,7 +798,7 @@ local_multijoincount <- function(w, df, permutations=999, #' @param permutations (optional) The number of permutations for the LISA #' computation #' @param permutation_method (optional) The permutation method used for the LISA -#' computation. Options are {'complete', 'lookup'}. Default is 'complete'. +#' computation. Options are ('complete', 'lookup'). Default is 'complete'. #' @param significance_cutoff (optional) A cutoff value for significance #' p-values to filter not-significant clusters #' @param cpu_threads (optional) The number of cpu threads used for parallel @@ -851,7 +851,7 @@ local_quantilelisa <- function(w, df, k, q, permutations=999, #' @param permutations (optional) The number of permutations for the LISA #' computation #' @param permutation_method (optional) The permutation method used for the LISA -#' computation. Options are {'complete', 'lookup'}. Default is 'complete'. +#' computation. Options are ('complete', 'lookup'). Default is 'complete'. #' @param significance_cutoff (optional) A cutoff value for significance #' p-values to filter not-significant clusters #' @param cpu_threads (optional) The number of cpu threads used for parallel @@ -918,11 +918,11 @@ local_multiquantilelisa <- function(w, df, k, q, permutations=999, #' @param df A subset of sf object with selected variables. #' E.g. guerry[c("Crm_prs", "Crm_prp", "Litercy")] #' @param k a positive integer number for k-nearest neighbors searching. -#' @param scale_method (optional) One of the scaling methods {'raw', -#' 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust'} to apply +#' @param scale_method (optional) One of the scaling methods ('raw', +#' 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust') to apply #' on input data. Default is 'standardize' (Z-score normalization). #' @param distance_method (optional) The type of distance metrics used to -#' measure the distance between input data. Options are {'euclidean', 'manhattan'}. Default is 'euclidean'. +#' measure the distance between input data. Options are ('euclidean', 'manhattan'). Default is 'euclidean'. #' @param power (optional) The power (or exponent) of a number says how many #' times to use the number in a multiplication. #' @param is_inverse (optional) FALSE (default) or TRUE, apply inverse on diff --git a/man/azp_greedy.Rd b/man/azp_greedy.Rd index 35b4b94c..486f800d 100644 --- a/man/azp_greedy.Rd +++ b/man/azp_greedy.Rd @@ -33,7 +33,7 @@ azp_greedy( \item{initial_regions}{(optional) The initial regions that the local search starts with. Default is empty. means the local search starts with a random process to "grow" clusters} -\item{scale_method}{(optional) One of the scaling methods {'raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust'} to apply on input data. Default is 'standardize' (Z-score normalization).} +\item{scale_method}{(optional) One of the scaling methods ('raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust') to apply on input data. Default is 'standardize' (Z-score normalization).} \item{distance_method}{(optional) The distance method used to compute the distance betwen observation i and j. Defaults to "euclidean". Options are "euclidean" and "manhattan"} diff --git a/man/azp_sa.Rd b/man/azp_sa.Rd index e8c2db4a..43ddd691 100644 --- a/man/azp_sa.Rd +++ b/man/azp_sa.Rd @@ -39,7 +39,7 @@ azp_sa( \item{initial_regions}{(optional) The initial regions that the local search starts with. Default is empty. means the local search starts with a random process to "grow" clusters} -\item{scale_method}{(optional) One of the scaling methods {'raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust'} to apply on input data. Default is 'standardize' (Z-score normalization).} +\item{scale_method}{(optional) One of the scaling methods ('raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust') to apply on input data. Default is 'standardize' (Z-score normalization).} \item{distance_method}{(optional) The distance method used to compute the distance betwen observation i and j. Defaults to "euclidean". Options are "euclidean" and "manhattan"} diff --git a/man/azp_tabu.Rd b/man/azp_tabu.Rd index c6be9de1..61e470c9 100644 --- a/man/azp_tabu.Rd +++ b/man/azp_tabu.Rd @@ -39,7 +39,7 @@ azp_tabu( \item{initial_regions}{(optional) The initial regions that the local search starts with. Default is empty. means the local search starts with a random process to "grow" clusters} -\item{scale_method}{(optional) One of the scaling methods {'raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust'} to apply on input data. Default is 'standardize' (Z-score normalization).} +\item{scale_method}{(optional) One of the scaling methods ('raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust') to apply on input data. Default is 'standardize' (Z-score normalization).} \item{distance_method}{(optional) The distance method used to compute the distance betwen observation i and j. Defaults to "euclidean". Options are "euclidean" and "manhattan"} diff --git a/man/local_bijoincount.Rd b/man/local_bijoincount.Rd index 79bed63f..5579c40c 100644 --- a/man/local_bijoincount.Rd +++ b/man/local_bijoincount.Rd @@ -24,7 +24,7 @@ E.g. guerry[c("TopCrm", "InvCrm")]} computation} \item{permutation_method}{(optional) The permutation method used for the -LISA computation. Options are {'complete', 'lookup'}. Default is 'complete'.} +LISA computation. Options are ('complete', 'lookup'). Default is 'complete'.} \item{significance_cutoff}{(optional) A cutoff value for significance p-values to filter not-significant clusters} diff --git a/man/local_bimoran.Rd b/man/local_bimoran.Rd index 5bae0103..3c7c1824 100644 --- a/man/local_bimoran.Rd +++ b/man/local_bimoran.Rd @@ -23,7 +23,7 @@ local_bimoran( computation} \item{permutation_method}{(optional) The permutation method used for the -LISA computation. Options are {'complete', 'lookup'}. Default is 'complete'.} +LISA computation. Options are ('complete', 'lookup'). Default is 'complete'.} \item{significance_cutoff}{(optional) A cutoff value for significance p-values to filter not-significant clusters} diff --git a/man/local_g.Rd b/man/local_g.Rd index 92705666..3a4b5e64 100644 --- a/man/local_g.Rd +++ b/man/local_g.Rd @@ -23,7 +23,7 @@ local_g( computation} \item{permutation_method}{(optional) The permutation method used for the -LISA computation. Options are {'complete', 'lookup'}. Default is 'complete'.} +LISA computation. Options are ('complete', 'lookup'). Default is 'complete'.} \item{significance_cutoff}{(optional) A cutoff value for significance p-values to filter not-significant clusters} diff --git a/man/local_geary.Rd b/man/local_geary.Rd index 58fd82dc..a42b78e6 100644 --- a/man/local_geary.Rd +++ b/man/local_geary.Rd @@ -23,7 +23,7 @@ local_geary( computation} \item{permutation_method}{(optional) The permutation method used for the -LISA computation. Options are {'complete', 'lookup'}. Default is 'complete'.} +LISA computation. Options are ('complete', 'lookup'). Default is 'complete'.} \item{significance_cutoff}{(optional) A cutoff value for significance p-values to filter not-significant clusters} diff --git a/man/local_gstar.Rd b/man/local_gstar.Rd index f9e4587a..95f05b3c 100644 --- a/man/local_gstar.Rd +++ b/man/local_gstar.Rd @@ -23,7 +23,7 @@ local_gstar( computation} \item{permutation_method}{(optional) The permutation method used for the -LISA computation. Options are {'complete', 'lookup'}. Default is 'complete'.} +LISA computation. Options are ('complete', 'lookup'). Default is 'complete'.} \item{significance_cutoff}{(optional) A cutoff value for significance p-values to filter not-significant clusters} diff --git a/man/local_joincount.Rd b/man/local_joincount.Rd index f55bba26..83a024cc 100644 --- a/man/local_joincount.Rd +++ b/man/local_joincount.Rd @@ -23,7 +23,7 @@ local_joincount( computation} \item{permutation_method}{(optional) The permutation method used for the -LISA computation. Options are {'complete', 'lookup'}. Default is 'complete'.} +LISA computation. Options are ('complete', 'lookup'). Default is 'complete'.} \item{significance_cutoff}{(optional) A cutoff value for significance p-values to filter not-significant clusters} diff --git a/man/local_moran.Rd b/man/local_moran.Rd index cbb1e1ae..6914f8cb 100644 --- a/man/local_moran.Rd +++ b/man/local_moran.Rd @@ -23,7 +23,7 @@ local_moran( computation} \item{permutation_method}{(optional) The permutation method used for the -LISA computation. Options are {'complete', 'lookup'}. Default is 'complete'.} +LISA computation. Options are ('complete', 'lookup'). Default is 'complete'.} \item{significance_cutoff}{(optional) A cutoff value for significance p-values to filter not-significant clusters} diff --git a/man/local_moran_eb.Rd b/man/local_moran_eb.Rd index 95d4c91b..1a9d806b 100644 --- a/man/local_moran_eb.Rd +++ b/man/local_moran_eb.Rd @@ -24,7 +24,7 @@ is "base" variable. E.g. guerry[c("hr60", "po60")]} computation} \item{permutation_method}{(optional) The permutation method used for the LISA -computation. Options are {'complete', 'lookup'}. Default is 'complete'.} +computation. Options are ('complete', 'lookup'). Default is 'complete'.} \item{significance_cutoff}{(optional) A cutoff value for significance p-values to filter not-significant clusters} diff --git a/man/local_multigeary.Rd b/man/local_multigeary.Rd index 335d6124..c828b533 100644 --- a/man/local_multigeary.Rd +++ b/man/local_multigeary.Rd @@ -23,7 +23,7 @@ local_multigeary( computation} \item{permutation_method}{(optional) The permutation method used for the -LISA computation. Options are {'complete', 'lookup'}. Default is 'complete'.} +LISA computation. Options are ('complete', 'lookup'). Default is 'complete'.} \item{significance_cutoff}{(optional) A cutoff value for significance p-values to filter not-significant clusters} diff --git a/man/local_multijoincount.Rd b/man/local_multijoincount.Rd index 92f7140d..0b78535a 100644 --- a/man/local_multijoincount.Rd +++ b/man/local_multijoincount.Rd @@ -24,7 +24,7 @@ E.g. guerry[c("TopCrm", "TopWealth", "TopLit")]} computation} \item{permutation_method}{(optional) The permutation method used for the -LISA computation. Options are {'complete', 'lookup'}. Default is 'complete'.} +LISA computation. Options are ('complete', 'lookup'). Default is 'complete'.} \item{significance_cutoff}{(optional) A cutoff value for significance p-values to filter not-significant clusters} diff --git a/man/local_multiquantilelisa.Rd b/man/local_multiquantilelisa.Rd index 69f7712d..1579bfbb 100644 --- a/man/local_multiquantilelisa.Rd +++ b/man/local_multiquantilelisa.Rd @@ -32,7 +32,7 @@ variable used in local join count statistics. Value stars from 1.} computation} \item{permutation_method}{(optional) The permutation method used for the LISA -computation. Options are {'complete', 'lookup'}. Default is 'complete'.} +computation. Options are ('complete', 'lookup'). Default is 'complete'.} \item{significance_cutoff}{(optional) A cutoff value for significance p-values to filter not-significant clusters} diff --git a/man/local_quantilelisa.Rd b/man/local_quantilelisa.Rd index eba096a8..55c53e7a 100644 --- a/man/local_quantilelisa.Rd +++ b/man/local_quantilelisa.Rd @@ -30,7 +30,7 @@ count statistics. Value stars from 1.} computation} \item{permutation_method}{(optional) The permutation method used for the LISA -computation. Options are {'complete', 'lookup'}. Default is 'complete'.} +computation. Options are ('complete', 'lookup'). Default is 'complete'.} \item{significance_cutoff}{(optional) A cutoff value for significance p-values to filter not-significant clusters} diff --git a/man/maxp_greedy.Rd b/man/maxp_greedy.Rd index 98a83e9c..9ccdb829 100644 --- a/man/maxp_greedy.Rd +++ b/man/maxp_greedy.Rd @@ -31,7 +31,7 @@ maxp_greedy( \item{initial_regions}{(optional): The initial regions that the local search starts with. Default is empty. means the local search starts with a random process to "grow" clusters} -\item{scale_method}{(optional) One of the scaling methods {'raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust'} to apply on input data. Default is 'standardize' (Z-score normalization).} +\item{scale_method}{(optional) One of the scaling methods ('raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust') to apply on input data. Default is 'standardize' (Z-score normalization).} \item{distance_method}{(optional) The distance method used to compute the distance betwen observation i and j. Defaults to "euclidean". Options are "euclidean" and "manhattan"} diff --git a/man/maxp_sa.Rd b/man/maxp_sa.Rd index a37bbcc0..38c97f58 100644 --- a/man/maxp_sa.Rd +++ b/man/maxp_sa.Rd @@ -37,7 +37,7 @@ maxp_sa( \item{initial_regions}{(optional): The initial regions that the local search starts with. Default is empty. means the local search starts with a random process to "grow" clusters} -\item{scale_method}{(optional) One of the scaling methods {'raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust'} to apply on input data. Default is 'standardize' (Z-score normalization).} +\item{scale_method}{(optional) One of the scaling methods ('raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust') to apply on input data. Default is 'standardize' (Z-score normalization).} \item{distance_method}{(optional) The distance method used to compute the distance betwen observation i and j. Defaults to "euclidean". Options are "euclidean" and "manhattan"} diff --git a/man/maxp_tabu.Rd b/man/maxp_tabu.Rd index 5c4533c3..d1a94367 100644 --- a/man/maxp_tabu.Rd +++ b/man/maxp_tabu.Rd @@ -37,7 +37,7 @@ maxp_tabu( \item{initial_regions}{(optional): The initial regions that the local search starts with. Default is empty. means the local search starts with a random process to "grow" clusters} -\item{scale_method}{(optional) One of the scaling methods {'raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust'} to apply on input data. Default is 'standardize' (Z-score normalization).} +\item{scale_method}{(optional) One of the scaling methods ('raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust') to apply on input data. Default is 'standardize' (Z-score normalization).} \item{distance_method}{(optional) The distance method used to compute the distance betwen observation i and j. Defaults to "euclidean". Options are "euclidean" and "manhattan"} diff --git a/man/neighbor_match_test.Rd b/man/neighbor_match_test.Rd index a7081650..ed147acc 100644 --- a/man/neighbor_match_test.Rd +++ b/man/neighbor_match_test.Rd @@ -21,12 +21,12 @@ E.g. guerry[c("Crm_prs", "Crm_prp", "Litercy")]} \item{k}{a positive integer number for k-nearest neighbors searching.} -\item{scale_method}{(optional) One of the scaling methods {'raw', -'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust'} to apply +\item{scale_method}{(optional) One of the scaling methods ('raw', +'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust') to apply on input data. Default is 'standardize' (Z-score normalization).} \item{distance_method}{(optional) The type of distance metrics used to -measure the distance between input data. Options are {'euclidean', 'manhattan'}. Default is 'euclidean'.} +measure the distance between input data. Options are ('euclidean', 'manhattan'). Default is 'euclidean'.} \item{power}{(optional) The power (or exponent) of a number says how many times to use the number in a multiplication.} diff --git a/man/redcap.Rd b/man/redcap.Rd index 487f331d..473aa4b6 100644 --- a/man/redcap.Rd +++ b/man/redcap.Rd @@ -31,7 +31,7 @@ redcap( \item{min_bound}{(optional) A minimum bound value that applies to all clusters} -\item{scale_method}{(optional) One of the scaling methods {'raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust'} to apply on input data. Default is 'standardize' (Z-score normalization).} +\item{scale_method}{(optional) One of the scaling methods ('raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust') to apply on input data. Default is 'standardize' (Z-score normalization).} \item{distance_method}{(optional) The distance method used to compute the distance betwen observation i and j. Defaults to "euclidean". Options are "euclidean" and "manhattan"} diff --git a/man/schc.Rd b/man/schc.Rd index f1aa4684..f728d88a 100644 --- a/man/schc.Rd +++ b/man/schc.Rd @@ -29,7 +29,7 @@ schc( \item{min_bound}{(optional) A minimum bound value that applies to all clusters} -\item{scale_method}{One of the scaling methods {'raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust'} to apply on input data. Default is 'standardize' (Z-score normalization).} +\item{scale_method}{One of the scaling methods ('raw', 'standardize', 'demean', 'mad', 'range_standardize', 'range_adjust') to apply on input data. Default is 'standardize' (Z-score normalization).} \item{distance_method}{(optional) The distance method used to compute the distance betwen observation i and j. Defaults to "euclidean". Options are "euclidean" and "manhattan"} diff --git a/man/skater.Rd b/man/skater.Rd index 4674e456..97a94d63 100644 --- a/man/skater.Rd +++ b/man/skater.Rd @@ -30,8 +30,8 @@ E.g. guerry[c("Crm_prs", "Crm_prp", "Litercy")]} \item{min_bound}{(optional) A minimum bound value that applies to all clusters} -\item{scale_method}{One of the scaling methods {'raw', 'standardize', -'demean', 'mad', 'range_standardize', 'range_adjust'} to apply on input data. +\item{scale_method}{One of the scaling methods ('raw', 'standardize', +'demean', 'mad', 'range_standardize', 'range_adjust') to apply on input data. Default is 'standardize' (Z-score normalization).} \item{distance_method}{(optional) The distance method used to compute the diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp index 8a2d257b..acaebdaf 100644 --- a/src/RcppExports.cpp +++ b/src/RcppExports.cpp @@ -5,6 +5,11 @@ using namespace Rcpp; +#ifdef RCPP_USE_GLOBAL_ROSTREAM +Rcpp::Rostream& Rcpp::Rcout = Rcpp::Rcpp_cout_get(); +Rcpp::Rostream& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get(); +#endif + // p_skater Rcpp::List p_skater(int k, SEXP xp_w, Rcpp::List& data, int n_vars, std::string scale_method, std::string distance_method, NumericVector& bound_vals, double min_bound, int seed, int cpu_threads, NumericVector& rdist); RcppExport SEXP _rgeoda_p_skater(SEXP kSEXP, SEXP xp_wSEXP, SEXP dataSEXP, SEXP n_varsSEXP, SEXP scale_methodSEXP, SEXP distance_methodSEXP, SEXP bound_valsSEXP, SEXP min_boundSEXP, SEXP seedSEXP, SEXP cpu_threadsSEXP, SEXP rdistSEXP) {