Updated some things

biometryhub · Mar 28, 2024 · 1acb8f6 · 1acb8f6
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diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,16 @@
+# biometryassist 1.1.4
+
+## Minor changes
+
+- Implemented the ability to plot designs with buffer plots 
+
+## Bug fixes
+
+- 
+
+
+
+
 # biometryassist 1.1.3
 
 ## Bug fixes

diff --git a/R/autoplot.R b/R/autoplot.R
@@ -99,7 +99,7 @@ autoplot.design <- function(object, rotation = 0, size = 4, margin = FALSE, pale
         object <- object$design
     }
     rlang::check_dots_used()
-    ntrt <- nlevels(as.factor(object$treatments))
+    ntrt <- nlevels(as.factor(as.character(object$treatments)))
 
     # create the colours for the graph
     if(palette == "default") {
@@ -128,8 +128,11 @@ autoplot.design <- function(object, rotation = 0, size = 4, margin = FALSE, pale
     else {
         stop("Invalid value for palette.")
     }
+
+    # object$treatments <- as.factor(as.character(object$treatments))
+
     hcl <- farver::decode_colour(colour_palette, "rgb", "hcl")
-    cols <- data.frame(treatments = levels(as.factor(object$treatments)),
+    cols <- data.frame(treatments = levels(object$treatments),
                        text_col = ifelse(hcl[, "l"] > 50, "black", "white"))
     object <- merge(object, cols)
 

diff --git a/R/create_buffers.R b/R/create_buffers.R
@@ -1,4 +1,4 @@
-#' Title
+#' Create buffers for design plots
 #'
 #' @param design The data frame of the design.
 #' @param type The type of buffer. One of edge, row, column, double row, double column, or block (coming soon).
@@ -30,7 +30,7 @@ create_buffers <- function(design, type, blocks = FALSE) {
         min_row <- min(design$row)
         min_col <- min(design$col)
 
-        row <- rep(seq(min_row, (2*nrow)+1, by = 2), each = ncol)
+        row <- rep(seq(min_row-1, (2*nrow)+1, by = 2), each = ncol)
         col <- rep(seq(1, ncol),times = nrow+1)
         n_brow <- length(row)  # Number of buffer rows
         treatments <- rep("buffer", n_brow)

diff --git a/man/biometryassist.Rd b/man/biometryassist.Rd
diff --git a/man/create_buffers.Rd b/man/create_buffers.Rd
diff --git a/tests/testthat/_snaps/all-w2.md b/tests/testthat/_snaps/all-w2.md
@@ -119,12 +119,12 @@
 ---
 
        Genotype predicted.value std.error    groups   ci  low   up
-    1       G04            4.15      0.14         a 0.23 3.92 4.37
+    1       G04            4.14      0.14         a 0.23 3.92 4.37
     2       G14            4.63      0.14        ab 0.23 4.41 4.86
     3       G20            4.80      0.14        bc 0.23 4.57 5.02
     4       G10            4.81      0.14       bcd 0.23 4.59 5.04
     5       G28            4.84      0.14      bcde 0.23 4.61 5.07
-    6       G24            4.86      0.14     bcdef 0.23 4.63 5.08
+    6       G24            4.85      0.14     bcdef 0.23 4.63 5.08
     7       G01            4.91      0.14    bcdefg 0.23 4.68 5.14
     8       G05            4.94      0.14   bcdefgh 0.23 4.72 5.17
     9       G49            4.95      0.14   bcdefgh 0.23 4.72 5.17
@@ -141,13 +141,13 @@
     20      G06            5.13      0.14  bcdefghi 0.23 4.90 5.35
     21      G55            5.14      0.14  bcdefghi 0.23 4.92 5.37
     22      G32            5.16      0.14 bcdefghij 0.23 4.93 5.38
-    23      G11            5.17      0.14 bcdefghij 0.23 4.94 5.39
+    23      G11            5.16      0.14 bcdefghij 0.23 4.94 5.39
     24      G39            5.18      0.14 bcdefghij 0.23 4.95 5.40
     25      G61            5.20      0.14 bcdefghij 0.23 4.97 5.42
     26      G53            5.21      0.14 bcdefghij 0.23 4.98 5.43
     27      G37            5.21      0.14 bcdefghij 0.23 4.99 5.44
     28      G26            5.21      0.14 bcdefghij 0.23 4.99 5.44
-    29      G43            5.22      0.14 bcdefghij 0.23 4.99 5.44
+    29      G43            5.21      0.14 bcdefghij 0.23 4.99 5.44
     30      G35            5.22      0.14 bcdefghij 0.23 4.99 5.44
     31      G66            5.22      0.14 bcdefghij 0.23 4.99 5.44
     32      G16            5.23      0.14  cdefghij 0.23 5.00 5.45
@@ -157,24 +157,24 @@
     36      G47            5.27      0.14  cdefghij 0.23 5.05 5.50
     37      G44            5.29      0.14  cdefghij 0.23 5.06 5.52
     38      G23            5.29      0.14  cdefghij 0.23 5.07 5.52
-    39      G56            5.30      0.14  cdefghij 0.23 5.07 5.52
+    39      G56            5.29      0.14  cdefghij 0.23 5.07 5.52
     40      G58            5.31      0.14  cdefghij 0.23 5.08 5.53
-    41      G57            5.32      0.14  cdefghij 0.23 5.09 5.54
+    41      G57            5.31      0.14  cdefghij 0.23 5.09 5.54
     42      G63            5.32      0.14  cdefghij 0.23 5.09 5.54
     43      G62            5.32      0.14  cdefghij 0.23 5.09 5.55
     44      G54            5.33      0.14  cdefghij 0.23 5.11 5.56
     45      G51            5.36      0.14  cdefghij 0.23 5.13 5.58
     46      G67            5.37      0.14  cdefghij 0.23 5.14 5.59
-    47      G59            5.37      0.14  cdefghij 0.23 5.14 5.60
+    47      G22            5.37      0.14  cdefghij 0.23 5.14 5.60
     48      G42            5.37      0.14  cdefghij 0.23 5.14 5.60
-    49      G22            5.37      0.14  cdefghij 0.23 5.14 5.60
+    49      G59            5.37      0.14  cdefghij 0.23 5.14 5.60
     50      G65            5.38      0.14  cdefghij 0.23 5.15 5.60
     51      G69            5.38      0.14  cdefghij 0.23 5.16 5.61
     52      G38            5.38      0.14  cdefghij 0.23 5.16 5.61
     53      G12            5.39      0.14   defghij 0.23 5.17 5.62
     54      G31            5.41      0.14    efghij 0.23 5.19 5.64
     55      G50            5.42      0.14    efghij 0.23 5.20 5.65
-    56      G17            5.43      0.14    efghij 0.23 5.20 5.65
+    56      G17            5.42      0.14    efghij 0.23 5.20 5.65
     57      G52            5.43      0.14    efghij 0.23 5.20 5.65
     58      G64            5.44      0.14     fghij 0.23 5.21 5.67
     59      G13            5.45      0.14      ghij 0.23 5.22 5.67
@@ -183,12 +183,12 @@
     62      G60            5.48      0.14      ghij 0.23 5.25 5.71
     63      G27            5.49      0.14     ghijk 0.23 5.26 5.72
     64      G18            5.50      0.14     ghijk 0.23 5.27 5.72
-    65      G36            5.51      0.14      hijk 0.23 5.28 5.73
+    65      G36            5.50      0.14      hijk 0.23 5.28 5.73
     66      G48            5.51      0.14      hijk 0.23 5.29 5.74
     67      G40            5.53      0.14      hijk 0.23 5.30 5.75
     68      G33            5.61      0.14       ijk 0.23 5.38 5.83
     69      G19            5.73      0.14        jk 0.23 5.51 5.96
-    70      G03            6.08      0.14         k 0.23 5.85 6.30
+    70      G03            6.07      0.14         k 0.23 5.85 6.30
 
 ---
 

diff --git a/tests/testthat/_snaps/all-w2/example5lmmautoplot1.svg b/tests/testthat/_snaps/all-w2/example5lmmautoplot1.svg
diff --git a/vario for dsum - seeing how it could work.r b/vario for dsum - seeing how it could work.r