v1.2.0.9002

- fix: Replace `rgdal` functions with ones from `sf` package, Issue \#44 - refactor: Remove XLConnect, Issue \#48 - DESCRIPTION, Suggests - MBSStools_vignette - fixe: Vignette now builds, Issue \#33
leppott · Oct 15, 2024 · 76c8b01 · 76c8b01
1 parent be09e1f
commit 76c8b01
Show file tree

Hide file tree

Showing 12 changed files with 1,845 additions and 3,154 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -4,7 +4,7 @@ Description: Suite of tools for data manipulation and calculations for Maryland
     DNR MBSS program.  Includes functions for calculating FIBI, BIBI (MBSS 
     genus), BIBI (MSW family), PHI, flow sums, ion contributions, and taxa 
     distribution maps.
-Version: 1.2.0.9001
+Version: 1.2.0.9002
 Authors@R: c(
   person("Erik W.", "Leppo", email="[email protected]", role=c("aut","cre")),
   person("Ann","Roseberry Lincoln", role="ctb"),
@@ -14,10 +14,9 @@ Depends: R (>= 3.4.0)
 License: GPL (>= 3)
 Encoding: UTF-8
 URL: https://github.com/leppott/MBSStools
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Imports: 
-    dplyr,
-    rgdal
+    dplyr
 Suggests: 
     DT,
     ggplot2,
@@ -30,8 +29,7 @@ Suggests:
     shiny,
     shinyjs,
     sp,
-    testthat,
-    XLConnect
+    testthat
 VignetteBuilder: knitr
 LazyData: true
 BugReports: https://github.com/leppott/MBSStools/issues
diff --git a/NEWS b/NEWS
@@ -3,7 +3,15 @@ NEWS-MBSStools
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
-    #> Last Update: 2024-04-08 12:38:08.080495
+    #> Last Update: 2024-10-15 12:37:10.670714
+
+# MBSStools v1.2.0.9002 (2024-04-08)
+
+- fix: Replace `rgdal` functions with ones from `sf` package, Issue \#44
+- refactor: Remove XLConnect, Issue \#48
+  - DESCRIPTION, Suggests
+  - MBSStools_vignette
+- fixe: Vignette now builds, Issue \#33
 
 # MBSStools v1.2.0.9001 (2024-04-08)
 

diff --git a/NEWS.md b/NEWS.md
@@ -3,7 +3,15 @@ NEWS-MBSStools
 
 <!-- NEWS.md is generated from NEWS.Rmd. Please edit that file -->
 
-    #> Last Update: 2024-04-08 12:38:08.080495
+    #> Last Update: 2024-10-15 12:37:10.670714
+
+# MBSStools v1.2.0.9002 (2024-04-08)
+
+- fix: Replace `rgdal` functions with ones from `sf` package, Issue \#44
+- refactor: Remove XLConnect, Issue \#48
+  - DESCRIPTION, Suggests
+  - MBSStools_vignette
+- fixe: Vignette now builds, Issue \#33
 
 # MBSStools v1.2.0.9001 (2024-04-08)
 

diff --git a/NEWS.rmd b/NEWS.rmd
@@ -17,6 +17,15 @@ knitr::opts_chunk$set(
 cat(paste0("Last Update: ",Sys.time()))
 ```
 
+MBSStools v1.2.0.9002 (2024-04-08)
+================
+
+* fix: Replace `rgdal` functions with ones from `sf` package, Issue #44
+* refactor: Remove XLConnect, Issue #48
+    + DESCRIPTION, Suggests
+    + MBSStools_vignette
+* fixe: Vignette now builds, Issue #33
+
 MBSStools v1.2.0.9001 (2024-04-08)
 ================
 * fix: Update examples and vignette to not use droplevels()

diff --git a/R/MapTaxaObs.R b/R/MapTaxaObs.R
@@ -14,7 +14,9 @@
 #' Tests for existence of Data, GIS directories and required files. On failure,
 #' stops and prints missing directories/files to screen.
 #'
-#' The R libraries rgdal, sf, and readxl are required for this function.
+#' The R libraries `rgdal`, `sf`, and `readxl` are required for this function.
+#' The `rgdal` package was deprecated in 2023.  In 2024 revised this fucntion to
+#' use functions from the `sf` package.
 #'
 #' @param obs Excel file containing 3 columns: TaxaName, Latitude83, Longitude83
 #' @param xWalk Crosswalk (Excel file) of taxa names between taxa name in
@@ -71,6 +73,9 @@
 #'
 #' # Create maps
 #' MapTaxaObs(obs, xWalk, dirMain)
+#'
+#' # Open folder (Windows only)
+#' # shell.exec(tempdir())
 #
 #' @export
 MapTaxaObs <- function(obs
@@ -123,8 +128,6 @@ MapTaxaObs <- function(obs
       # shell.exec(dirMain)
     }## IF ~ boo_QC ~ END
 
-
-
     # 2021-01-10
     # Define missing variables
     # bindings for global variables -----
@@ -273,15 +276,6 @@ MapTaxaObs <- function(obs
     ppi <- 72
     #dsn<-paste(dirMain,dirGIS,sep="/")
     dsn <- file.path(dirMain, dirGIS)
-    # state     <- rgdal::readOGR(dsn = dsn
-    #                             , layer = "MD_State_Boundary"
-    #                             , verbose=verbose)
-    # coastline <- rgdal::readOGR(dsn = dsn
-    #                             , layer = "MD_Coast_Hydrology"
-    #                             , verbose=verbose)
-    # counties  <- rgdal::readOGR(dsn = dsn
-    #                             , layer = "MD_Boundary_County_Detailed"
-    #                             , verbose=verbose)
 
     # sf version
     state     <- sf::st_read(dsn = dsn
@@ -307,30 +301,39 @@ MapTaxaObs <- function(obs
                      , pointsize = 12
                      , bg = "white")
         plot(sf::st_geometry(state)
-             , col="white"
+             , col = "white"
              , border = "gray")
         plot(sf::st_geometry(coastline)
              , add = TRUE
              , col = "light blue"
-             , border=FALSE)
+             , border = FALSE)
         plot(sf::st_geometry(counties)
              , add = TRUE
              , col = "white"
              , border = "darkslategray"
              , lwd = 0.5)
-        #xy <- df.taxon.sites[,2:3]
-        proj.sites <- rgdal::project(cbind(df.taxon.sites$Longitude83
-                                           , df.taxon.sites$Latitude83)
-                                     ,
-        "+proj=lcc +lat_1=39.45 +lat_2=38.3 +lat_0=37.66666666666666 +lon_0=-77
-                +x_0=400000 +y_0=0 +datum=NAD83 +units=m +no_defs")
-        graphics::points(proj.sites[, 1]
-                         , proj.sites[, 2]
-                         , pch = 21
-                         , col = "black"
-                         , bg = "green"
-                         , cex = 1.0)
+
+        ### sites
+        # 4326, WGS 84
+        # 6487, NAD83(2011)/Maryland in meters
+        # 6488, NAD83(2011)/Maryland in US survey feet
+        # 26985, NAD83/Maryland                             *this one*
+        # 2248
+        sites_wgs84 <- sf::st_as_sf(df.taxon.sites,
+                                    coords = c("Longitude83", "Latitude83"),
+                                    crs = 4326)
+        sites_nad83md_m <- sf::st_transform(sites_wgs84, crs = 26985)
+        #### plot
+        plot(sites_nad83md_m,
+             pch = 21,
+             col = "black",
+             bg  = "green",
+             cex = 1.0,
+             type = "p",
+             add = TRUE)
+
       grDevices::dev.off()
+
       # user feedback
       if (verbose == TRUE) {##IF.verbose.START
         message(paste0("Saving map "
@@ -344,7 +347,7 @@ MapTaxaObs <- function(obs
       }##IF.verbose.END
       ##PLOT.END
     }##FOR.i.END
-    #
+
     # 6. Clean up ####
     # Number on Non-Matches
     n.nomatch <- nrow(df.taxa.nomatch)