moving vegan suggests #58

DESCRIPTION

@@ -45,10 +45,11 @@ Suggests:
     SoilTaxonomy,
     sf,
     Hmisc,
-    knitr
+    knitr,
+    vegan
 Depends: R (>= 3.5.0)
 Imports: grDevices, graphics, methods, stats, utils, aqp, ape, 
-  soilDB, cluster, lattice, vegan,
+  soilDB, cluster, lattice,
   reshape2, scales, circular, RColorBrewer, plyr, 
   digest, e1071, stringi, parallel, curl, grid
 Additional_repositories: https://hydromad.github.io

NAMESPACE

@@ -93,11 +93,6 @@ importFrom(e1071,
   skewness
 )
 
-importFrom(vegan,
-  decostand,
-  vegdist
-)
-
 importFrom(soilDB,
   format_SQL_in_statement,
   SDA_query,

NEWS.md

@@ -1,3 +1,6 @@
+# sharpshootR 2.3.1 (2024-05-29)
+ * 
+
 # sharpshootR 2.3 (2024-04-08)
  * CRAN release
  * `prepare_SSURGO_hydro_data()` now returns more soil property data

R/component.adj.matrix.R

@@ -102,13 +102,19 @@ component.adj.matrix <-function(d, mu = 'mukey', co = 'compname', wt = 'comppct_
   # default method, based on ideas from ecological community matrix analysis
   if(method == 'community.matrix') {
 
+    # this requires the vegan package
+    if(!requireNamespace('vegan')) {
+      stop('please install the vegan package', call. = FALSE)
+    }
+
     # sanity checks
-    if(is.null(wt))
+    if(is.null(wt)) {
       stop('must supply a column name containing weights')
-
+    }
+
     # reshape to component x mukey community matrix
     fm <- as.formula(paste(co, ' ~ ', mu, sep=''))
-    d.wide <- dcast(d, fm, value.var='weight', fill=0)
+    d.wide <- dcast(d, fm, value.var ='weight', fill = 0)
 
     # convert into community matrix by moving first column -> row.names
     d.mat <- as.matrix(d.wide[, -1])
@@ -124,9 +130,9 @@ component.adj.matrix <-function(d, mu = 'mukey', co = 'compname', wt = 'comppct_
     # convert community matrix into dissimilarity matrix
     # optional standardization
     if(standardization != 'none')
-      d.mat <- decostand(d.mat, method=standardization)
+      d.mat <- vegan::decostand(d.mat, method = standardization)
     # distance matrix
-    m <- vegdist(d.mat, method=metric)
+    m <- vegan::vegdist(d.mat, method = metric)
 
     # convert to similarity matrix: S = max(D) - D [Kaufman & Rousseeuw]
     if(similarity == TRUE) {

R/dailyWB.R

@@ -38,8 +38,10 @@
 dailyWB <- function(x, daily.data, id, MS.style = 'default', S_0 = 0.5, M = 0, etmult = 1) {
 
   # sanity check: package requirements
-  if(!requireNamespace('hydromad'))
+  if(!requireNamespace('hydromad')) {
     stop('please install the hydromad package', call. = FALSE)
+  }
+
 
   # sanity checks
   stopifnot(inherits(x, 'data.frame'))