R create an uneven (7 rows by 6 columns) transition matrix from a dataframe

Question

I am attempting to create a transition matrix for coral size class transitions that reflects the data in the following dataframe:

Dataframe Header

Full Dataframe

HAN_high_transition <- structure(list(experimental_treatment = c("Hanauma Bay_High", 
"Hanauma Bay_High", "Hanauma Bay_High", "Hanauma Bay_High", "Hanauma Bay_High", 
"Hanauma Bay_High", "Hanauma Bay_High", "Hanauma Bay_High", "Hanauma Bay_High", 
"Hanauma Bay_High", "Hanauma Bay_High", "Hanauma Bay_High", "Hanauma Bay_High", 
"Hanauma Bay_High", "Hanauma Bay_High", "Hanauma Bay_High", "Hanauma Bay_High", 
"Hanauma Bay_High", "Hanauma Bay_High", "Hanauma Bay_High", "Hanauma Bay_High", 
"Hanauma Bay_High", "Hanauma Bay_High", "Hanauma Bay_High", "Hanauma Bay_High", 
"Hanauma Bay_High", "Hanauma Bay_High", "Hanauma Bay_High", "Hanauma Bay_High", 
"Hanauma Bay_High", "Hanauma Bay_High", "Hanauma Bay_High", "Hanauma Bay_High", 
"Hanauma Bay_High", "Hanauma Bay_High", "Hanauma Bay_High", "Hanauma Bay_High", 
"Hanauma Bay_High", "Hanauma Bay_High", "Hanauma Bay_High", "Hanauma Bay_High", 
"Hanauma Bay_High"), size_class_start = c(1, 1, 1, 1, 1, 1, 1, 
2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 
5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6), size_class_end = c("1", 
"2", "3", "4", "5", "6", "M", "1", "2", "3", "4", "5", "6", "M", 
"1", "2", "3", "4", "5", "6", "M", "1", "2", "3", "4", "5", "6", 
"M", "1", "2", "3", "4", "5", "6", "M", "1", "2", "3", "4", "5", 
"6", "M"), mean_transition_prob = c(0.438576084409418, 0.335851494184828, 
0.0262626262626263, 0, 0, 0, 0.199309795143128, 0.0440412528647823, 
0.474382866094096, 0.397812733908991, 0.0291879837334383, 0, 
0, 0.0545751633986928, 0.00476190476190476, 0.0863888888888889, 
0.531626984126984, 0.272777777777778, 0.0166666666666667, 0.0111111111111111, 
0.0766666666666667, 0.01, 0, 0.0266666666666667, 0.587619047619048, 
0.358571428571429, 0.01, 0.00714285714285714, 0, 0, 0.1, 0.175, 
0.475, 0.216666666666667, 0.0333333333333333, 0, 0, 0, 0, 0.260416666666667, 
0.489583333333333, 0.25)), row.names = c(NA, -42L), groups = structure(list(
    experimental_treatment = c("Hanauma Bay_High", "Hanauma Bay_High", 
    "Hanauma Bay_High", "Hanauma Bay_High", "Hanauma Bay_High", 
    "Hanauma Bay_High"), size_class_start = c(1, 2, 3, 4, 5, 
    6), .rows = structure(list(1:7, 8:14, 15:21, 22:28, 29:35, 
        36:42), ptype = integer(0), class = c("vctrs_list_of", 
    "vctrs_vctr", "list"))), row.names = c(NA, -6L), class = c("tbl_df", 
"tbl", "data.frame"), .drop = TRUE), class = c("grouped_df", 
"tbl_df", "tbl", "data.frame"))

I would like to create a 7 row x 6 column transition matrix based on size_class_start (columns) and size_class_end (rows). Each size class (1-6) has the transition probabilities (mean_transition_prob) calculated for if it will stay in the same size class, grow, or shrink if the starting_size_class > 1. The 7th row represents the probability of mortality or "M".

I attempted to use the matrix() function but received the following error:

Attempted Code

col <- as.character(c(1, 2, 3, 4, 5, 6))
row <- as.character(c(1, 2, 3, 4, 5, 6, "M"))

m <- matrix(HAN_high_transition$mean_transition_prob, nrow = 7, ncol = 6, dimnames = list(HAN_high_transition$size_class_start, HAN_high_transition$size_class_end))

Error in matrix(HAN_high_transition$mean_transition_prob, nrow = 7, ncol = 6,  : 
  length of 'dimnames' [1] not equal to array extent

Let me know if there is a solution with tweaking this code or trying something else entirely. I am open to any and all suggestions. Thanks for your time!

Answer 1

When you fold a vector into a matrix, the default is to fill columns sequentially which is how your data is organized. You just needed to use Row and Col as your dimnames :

Row <- c(1:6, "M")
Col <- as.character(1:6)
transmat <- matrix(HAN_high_transition$mean_transition_prob, 7, 6, dimnames=list(Row, Col))
transmat
#            1          2           3           4          5         6
# 1 0.43857608 0.04404125 0.004761905 0.010000000 0.00000000 0.0000000
# 2 0.33585149 0.47438287 0.086388889 0.000000000 0.00000000 0.0000000
# 3 0.02626263 0.39781273 0.531626984 0.026666667 0.10000000 0.0000000
# 4 0.00000000 0.02918798 0.272777778 0.587619048 0.17500000 0.0000000
# 5 0.00000000 0.00000000 0.016666667 0.358571429 0.47500000 0.2604167
# 6 0.00000000 0.00000000 0.011111111 0.010000000 0.21666667 0.4895833
# M 0.19930980 0.05457516 0.076666667 0.007142857 0.03333333 0.2500000