submission cleanup

andrewmarx · Jul 5, 2024 · 802d6fb · 802d6fb
1 parent dd60d4d
commit 802d6fb
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Showing 7 changed files with 12 additions and 10 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -44,7 +44,7 @@ Imports:
     raster,
     terra (>= 1.7-3),
     circular
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Suggests: knitr,
     rmarkdown,
     testthat,

diff --git a/R/cond_passage.R b/R/cond_passage.R
@@ -52,7 +52,7 @@ NULL
 #' @template section-perf
 #'
 #' @template param-samc
-#' @param init Placeholder/not currently implemented.
+#' @template param-init
 #' @template param-origin
 #' @template param-dest
 #'

diff --git a/R/distribution.R b/R/distribution.R
@@ -120,8 +120,8 @@ setMethod(
 
       res = diag(pv) %*% res
 
-      res = apply(res, 1, function(x) samc:::.summarize_crw(samc_crw, x, sum))
-      res = apply(res, 1, function(x) samc:::.summarize_crw(samc_crw, x, sum)) # Same margin because results of last are transposed
+      res = apply(res, 1, function(x) samc:::.summarize_crw(samc, x, sum))
+      res = apply(res, 1, function(x) samc:::.summarize_crw(samc, x, sum)) # Same margin because results of last are transposed
     }
 
     return(res)

diff --git a/R/mortality.R b/R/mortality.R
@@ -178,8 +178,8 @@ setMethod(
 
       bt = diag(pv) %*% bt
 
-      bt = apply(bt, 1, function(x) samc:::.summarize_crw(samc_crw, x, sum))
-      bt = apply(bt, 1, function(x) samc:::.summarize_crw(samc_crw, x, sum)) # Same margin because results of last are transposed
+      bt = apply(bt, 1, function(x) samc:::.summarize_crw(samc, x, sum))
+      bt = apply(bt, 1, function(x) samc:::.summarize_crw(samc, x, sum)) # Same margin because results of last are transposed
     }
 
     return(bt)

diff --git a/R/samc-class.R b/R/samc-class.R
@@ -84,6 +84,7 @@ NULL
 #' @slot nodes The number of nodes in the graph
 #' @slot map Used to verify landscape inputs and mapping of vector data
 #' @slot crw_map Matrix used to map location and direction to edges description
+#' @slot prob_mat Matric for CRW probabilities
 #' @slot names Names of the transient states
 #' @slot clumps Number of discontinuous regions in data
 #' @slot override Used to prevent accidental use of memory intensive functions

diff --git a/R/survival.R b/R/survival.R
@@ -33,6 +33,7 @@ NULL
 #'
 #' @template param-samc
 #' @template param-init
+#' @template param-origin
 #'
 #' @return See Details
 #'

diff --git a/R/visitation.R b/R/visitation.R
@@ -174,8 +174,8 @@ setMethod(
 
       res = diag(pv) %*% res
 
-      res = apply(res, 1, function(x) samc:::.summarize_crw(samc_crw, x, sum))
-      res = apply(res, 1, function(x) samc:::.summarize_crw(samc_crw, x, sum)) # Same margin because results of last are transposed
+      res = apply(res, 1, function(x) samc:::.summarize_crw(samc, x, sum))
+      res = apply(res, 1, function(x) samc:::.summarize_crw(samc, x, sum)) # Same margin because results of last are transposed
     }
 
     return(res)
@@ -326,8 +326,8 @@ setMethod(
 
       n = diag(pv) %*% n
 
-      n = apply(n, 1, function(x) samc:::.summarize_crw(samc_crw, x, sum))
-      n = apply(n, 1, function(x) samc:::.summarize_crw(samc_crw, x, sum)) # Same margin because results of last are transposed
+      n = apply(n, 1, function(x) samc:::.summarize_crw(samc, x, sum))
+      n = apply(n, 1, function(x) samc:::.summarize_crw(samc, x, sum)) # Same margin because results of last are transposed
     }
 
     return(n)