From 802d6fbdcfceb85be6a54bebb13e20c9cec9c025 Mon Sep 17 00:00:00 2001 From: Andrew Marx Date: Fri, 5 Jul 2024 16:52:04 -0400 Subject: [PATCH] submission cleanup --- DESCRIPTION | 2 +- R/cond_passage.R | 2 +- R/distribution.R | 4 ++-- R/mortality.R | 4 ++-- R/samc-class.R | 1 + R/survival.R | 1 + R/visitation.R | 8 ++++---- 7 files changed, 12 insertions(+), 10 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 284d613..0129313 100644 --- 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 index c501646..ecae499 100644 --- 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 index 7732557..c9f18d2 100644 --- 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 index 819804c..e7eeb61 100644 --- 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 index 0c0891c..15d3c57 100644 --- 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 index 8d5ac7a..29cdb5e 100644 --- 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 index d8f9777..380ee5e 100644 --- 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)