`nnet::multinom` with wide format data

[vincentarelbundock]

The nnet::multinom function supports two different data formats: wide and long. The two approaches yield exactly identical estimates. However, the parameters package does not support the wide format:

library(nnet)
library(faraway)
data("cns", package = "faraway")

Long format works as expected

cns2 <- reshape(cns, direction = "long", timevar = "Type",
    times = names(cns)[3:5], varying = 3:5, v.names = "Freq")[, 3:6]
cns2$Type <- factor(cns2$Type, levels = unique(cns2$Type))
m2 <- multinom(Type ~ Water + Work, data = cns2, weights = Freq, trace = FALSE)
parameters::parameters(m2)
# # Response level: sp
# 
# Parameter        |  Log-Odds |       SE |        95% CI | t(42) |     p
# -----------------------------------------------------------------------
# (Intercept)      |      0.38 |     0.19 | [-0.01, 0.76] |  1.97 | 0.055
# Water            | -1.30e-03 | 2.03e-03 | [-0.01, 0.00] | -0.64 | 0.527
# Work [NonManual] |      0.12 |     0.21 | [-0.31, 0.54] |  0.55 | 0.582
# 
# # Response level: other
# 
# Parameter        | Log-Odds |       SE |         95% CI | t(42) |      p
# ------------------------------------------------------------------------
# (Intercept)      |    -1.12 |     0.28 | [-1.69, -0.56] | -4.02 | < .001
# Water            | 2.18e-03 | 2.90e-03 | [ 0.00,  0.01] |  0.75 | 0.455 
# Work [NonManual] |    -0.27 |     0.32 | [-0.93,  0.39] | -0.83 | 0.410

Wide format does not display properly (merge issue)

m1 <- multinom(cbind(An, Sp, Other) ~ Water + Work, data = cns, trace = FALSE)
parameters::parameters(m1)
# Warning in merge.data.frame(parameters, std_err, by = merge_by, sort = FALSE):
# column names 'Response.x', 'Response.y' are duplicated in the result
# Warning in merge.data.frame(parameters, statistic, by = merge_by, sort =
# FALSE): column names 'Response.x', 'Response.y' are duplicated in the result
#
# Parameter        |  Log-Odds |       SE |        95% CI | Response | t(10) |     p | Response.1
# -----------------------------------------------------------------------------------------------
# (Intercept)      |      0.38 |     0.19 | [-0.05, 0.80] |       Sp |  1.97 | 0.077 |         Sp
# Water            | -1.30e-03 | 2.03e-03 | [-0.01, 0.00] |       Sp | -0.64 | 0.538 |         Sp
# Work [NonManual] |      0.12 |     0.21 | [-0.35, 0.58] |       Sp |  0.55 | 0.591 |         Sp
# (Intercept)      |     -1.12 |     0.19 | [-0.05, 0.80] |       Sp |  1.97 | 0.077 |         Sp
# Water            |  2.18e-03 | 2.03e-03 | [-0.01, 0.00] |       Sp | -0.64 | 0.538 |         Sp
# WorkNonManual    |     -0.27 |     0.21 | [-0.35, 0.58] |       Sp |  0.55 | 0.591 |         Sp

Note that the two models are exactly equivalent:

coef(m1)
#       (Intercept)        Water WorkNonManual
# Sp      0.3752018 -0.001297048     0.1157557
# Other  -1.1225496  0.002182689    -0.2702791

coef(m2)
#       (Intercept)        Water WorkNonManual
# Sp      0.3752018 -0.001297048     0.1157557
# Other  -1.1225496  0.002182689    -0.2702791