release spEcula 0.1.3

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: spEcula
 Title: Spatial Prediction Methods In R
-Version: 0.1.2.9000
+Version: 0.1.3
 Authors@R: c(
     person("Wenbo", "Lv", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0009-0002-6003-3800")),

NAMESPACE

@@ -5,8 +5,15 @@ export(gos)
 export(gos_bestkappa)
 export(inverse_bcPower)
 export(sandwich)
+importFrom(dplyr,all_of)
+importFrom(dplyr,group_by)
+importFrom(dplyr,left_join)
+importFrom(dplyr,mutate)
+importFrom(dplyr,n)
+importFrom(dplyr,pick)
 importFrom(dplyr,select)
 importFrom(dplyr,summarise)
+importFrom(dplyr,ungroup)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,geom_line)
 importFrom(ggplot2,geom_point)
@@ -21,7 +28,16 @@ importFrom(parallel,makeCluster)
 importFrom(parallel,parLapply)
 importFrom(parallel,stopCluster)
 importFrom(purrr,map_dfr)
+importFrom(sf,st_area)
+importFrom(sf,st_as_sf)
+importFrom(sf,st_drop_geometry)
+importFrom(sf,st_geometry)
+importFrom(sf,st_intersection)
+importFrom(sf,st_join)
+importFrom(sf,st_union)
 importFrom(stats,as.formula)
 importFrom(stats,quantile)
 importFrom(stats,sd)
+importFrom(stats,var)
 importFrom(tibble,as_tibble)
+importFrom(tidyr,replace_na)

NEWS.md

@@ -2,6 +2,10 @@
 
 * support more advanced spatial methods.
 
+# spEcula 0.1.3
+
+* Remove spatial hierarchical heterogeneity test, please consider the [**gdverse**](https://spatlyu.github.io/gdverse) package for related functions.
+
 # spEcula 0.1.2
 
 * Support GOS and sandwich mapping model.

R/gos.R

@@ -209,7 +209,6 @@ gos_bestkappa = \(formula, data = NULL, kappa = seq(0.05,1,0.05),
   cv.out = out_rmse %>%
     dplyr::summarise(rmse = mean(rmse,na.rm = T),
                      .by = kappa)
-
   k = which(cv.out$rmse == min(cv.out$rmse))[1]
   best_kappa = cv.out$kappa[k]
 
@@ -227,11 +226,9 @@ gos_bestkappa = \(formula, data = NULL, kappa = seq(0.05,1,0.05),
                                            max(cv.out$rmse))) +
     ggplot2::theme_bw()
 
-
   out = list("bestkappa" = best_kappa,
              "cvrmse" = out_rmse,
              "cvmean" = cv.out,
              "plot" = p1)
-
   return(out)
 }

R/sandwich.R

@@ -16,6 +16,10 @@
 #' Default is `area`.
 #'
 #' @return A `sf` object with estimated mean `sandwichest_mean` and standard error `sandwichest_standarderror`.
+#' @importFrom sf st_as_sf st_join st_drop_geometry st_intersection st_union
+#' @importFrom dplyr group_by pick group_by summarise n ungroup select left_join mutate all_of
+#' @importFrom tidyr replace_na
+#' @importFrom stats var
 #' @export
 #'
 #' @examples

R/spEcula_helper.R

@@ -31,6 +31,7 @@ CalRMSE = \(yobse,ypred){
 }
 
 #' @title Rename sf object geometry name
+#' @importFrom sf st_geometry
 #' @noRd
 st_rename_geometry = \(g, name){
   current = attr(g, "sf_column")
@@ -40,6 +41,7 @@ st_rename_geometry = \(g, name){
 }
 
 #' @title Calculate the area of the polygon element using the specified unit
+#' @importFrom sf st_area
 #' @noRd
 st_geographical_area = \(g){
   garea = g %>%

README.Rmd

@@ -26,6 +26,19 @@ knitr::opts_chunk$set(
 
 The goal of **spEcula** is to make it easier to use **R** for **spatial prediction** based on **various spatial relationships** (e.g. spatial dependence, spatial heterogeneity and geographical similarity).
 
+## Overview
+
+Full document of the most recent release of **spEcula** is online:
+<https://spatlyu.github.io/spEcula/>
+
+Current models and functions provided by **spEcula** are:
+
+|   **spatial prediction method**   |   **spEcula function**   |   **support status**   |
+|-----------------------------------|--------------------------|------------------------|
+|  Geographically Optimal Similarity  |        `gos()`         |          ✔️        |
+|  Sandwich Mapping Model  |        `sandwich()`         |          ✔️        |
+
+
 ## Installation
 
 You can install the development version of *spEcula* from [*github*](https://github.com/SpatLyu/spEcula):
@@ -89,20 +102,6 @@ plot_grid(f1,f2,nrow = 1,label_fontfamily = 'serif',
 p
 ```
 
-### Spatial Stratified Heterogeneity Test
-
-```{r example_ssh_test}
-library(spEcula)
-data(NTDs)
-head(NTDs)
-```
-
-```{r}
-fd = ssh.test(incidence ~ watershed + elevation + soiltype,
-              data = NTDs,type = 'factor')
-fd
-```
-
 ### Sandwich Mapping Model
 
 ```{r sandwich,fig.width=5.5,fig.height=3.5}

README.md

@@ -14,6 +14,18 @@ The goal of **spEcula** is to make it easier to use **R** for **spatial
 prediction** based on **various spatial relationships** (e.g. spatial
 dependence, spatial heterogeneity and geographical similarity).
 
+## Overview
+
+Full document of the most recent release of **spEcula** is online:
+<https://spatlyu.github.io/spEcula/>
+
+Current models and functions provided by **spEcula** are:
+
+| **spatial prediction method**     | **spEcula function** | **support status** |
+|-----------------------------------|----------------------|--------------------|
+| Geographically Optimal Similarity | `gos()`              | ✔️                 |
+| Sandwich Mapping Model            | `sandwich()`         | ✔️                 |
+
 ## Installation
 
 You can install the development version of *spEcula* from
@@ -45,7 +57,7 @@ tictoc::tic()
 g1 = gos(Zn ~ Slope + Water + NDVI  + SOC + pH + Road + Mine,
          data = zn, newdata = grid, kappa = 0.08,cores = 6)
 tictoc::toc()
-## 6.85 sec elapsed
+## 6.6 sec elapsed
 ```
 
 ``` r
@@ -99,38 +111,6 @@ p
 
 <img src="man/figures/README-gos_result-1.png" width="100%" />
 
-### Spatial Stratified Heterogeneity Test
-
-``` r
-library(spEcula)
-data(NTDs)
-head(NTDs)
-## # A tibble: 6 × 5
-##   SP_ID incidence watershed elevation soiltype
-##   <chr>     <dbl>     <int>     <int>    <int>
-## 1 0          5.94         5         5        5
-## 2 1          5.87         5         5        4
-## 3 2          5.88         5         5        5
-## 4 3          5.98         5         5        5
-## 5 4          5.96         5         5        1
-## 6 5          5.66         5         5        4
-```
-
-``` r
-fd = ssh.test(incidence ~ watershed + elevation + soiltype,
-              data = NTDs,type = 'factor')
-fd
-## Spatial Stratified Heterogeneity Test 
-##  
-##           Factor detector
-```
-
-| variable  | Q-statistic |  P-value  |
-|:---------:|:-----------:|:---------:|
-| watershed |   0.6378    | 0.0001288 |
-| elevation |   0.6067    |  0.04338  |
-| soiltype  |   0.3857    |  0.3721   |
-
 ### Sandwich Mapping Model
 
 ``` r