Merge pull request #46 from biometryhub/dev

Merging dev into main

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
 Version: 1.1.1
-Date: 2022-10-26 01:28:34 UTC
-SHA: 42ae12787fb62f4ad72217cdaf6053bacd9507c4
+Date: 2022-10-27 10:44:28 UTC
+SHA: 4929289d7c537d15a20641dd846608ce65c705c9

DESCRIPTION

@@ -24,7 +24,13 @@ Authors@R:
 Description: Provides functions to aid in the design and analysis of
     agronomic and agricultural experiments through easy access to
     documentation and helper functions, especially for users who are
-    learning these concepts.
+    learning these concepts. While not required for most functionality,
+    this package enhances the `asreml` package which provides a 
+    computationally efficient algorithm for fitting mixed models 
+    using Residual Maximum Likelihood. It is a commercial package 
+    that can be purchased as 'asreml-R' from 'VSNi' 
+    <https://vsni.co.uk/>, who will supply a zip file for local 
+    installation/updating (see <https://asreml.kb.vsni.co.uk/>). 
 License: MIT + file LICENSE
 URL: https://biometryhub.github.io/biometryassist/
 BugReports: https://github.com/biometryhub/biometryassist/issues

R/mct.R

@@ -30,7 +30,7 @@
 #'
 #' @return A list containing a data frame with predicted means, standard errors, confidence interval upper and lower bounds, and significant group allocations (named `predicted_values`), as well as a plot visually displaying the predicted values (named `predicted_plot`). If some of the predicted values are aliased, a warning is printed, and the aliased treatment levels are returned in the output (named `aliased`).
 #'
-#' @references Jørgensen, E. & Pedersen, A. R. How to Obtain Those Nasty Standard Errors From Transformed Data - and Why They Should Not Be Used.
+#' @references Jørgensen, E. & Pedersen, A. R. (1997). How to Obtain Those Nasty Standard Errors From Transformed Data - and Why They Should Not Be Used. [<https://pure.au.dk/portal/en/publications/how-to-obtain-those-nasty-standard-errors-from-transformed-data--and-why-they-should-not-be-used(d649ca20-d15f-11db-8e26-000ea68e967b).html>](https://pure.au.dk/portal/en/publications/how-to-obtain-those-nasty-standard-errors-from-transformed-data--and-why-they-should-not-be-used(d649ca20-d15f-11db-8e26-000ea68e967b).html)
 #'
 #' @examples
 #' # Fit aov model

R/variogram.r

@@ -197,12 +197,13 @@ vario_df <- function(model.obj, Row = NA, Column = NA) {
                 row <- Row[val_index] + offset[1]
                 col <- Column[val_index] + offset[2]
 
-                if (0 < row && row <= nrows && 0 < col && col <= ncols) {
-                    other <- ifelse(!is.na(Resid[Row == row & Column == col]),
-                                    Resid[Row == row & Column == col],
-                                    0)
-                    gamma <- gamma + (Resid[val_index]-other)^2
-                    np <- np + 1
+                if (0 < row && row <= nrows && 0 < col && col <= ncols && !is.na(Resid[val_index])) {
+                    other <- Resid[Row == row & Column == col]
+
+                    if (!is.na(other)) {
+                        gamma <- gamma + (Resid[val_index] - other)^2
+                        np <- np + 1
+                    }
                 }
             }
         }
@@ -217,6 +218,7 @@ vario_df <- function(model.obj, Row = NA, Column = NA) {
         gammas[index] <- gamma
         nps[index] <- np
     }
+    nps[1] <- nps[1]-sum(is.na(Resid))
     vario <- cbind(vario, data.frame(gamma = gammas, np = nps))
     colnames(vario) <- c(dims, "gamma", "np")
     class(vario) <- c("variogram", "data.frame")

cran-comments.md

@@ -1,3 +1,11 @@
+## Resubmission
+This is a resubmission. In this version I have:
+
+* Explained in the DESCRIPTION where the enhanced package asreml can be obtained.
+
+* I have also added a URL to the reference in the `multiple_comparisons()` function documentation.
+
+
 ## Test environments
 * Local Windows 10 install, R 4.2.1
 * Ubuntu 22.04 (Virtual Machine), R 4.2.1