diff --git a/README.Rmd b/README.Rmd
index be6c315..95a06cb 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -164,12 +164,8 @@ summary(ans)
Or better, we can use `texreg` to generate a pretty output:
```{r mle-out, echo=FALSE, results='asis'}
-texreg::createTexreg(
- coef.names = names(coef(ans)),
- coef = coef(ans),
- se = sqrt(diag(vcov(ans))),
- gof.names = c("AIC", "BIC", "N"), gof = c(AIC(ans), BIC(ans), nobs(ans)), gof.decimal = c(T,T,F)
-) |> texreg::knitreg(single.row = TRUE)
+summary_table(ans, as_texreg=TRUE) |>
+ texreg::knitreg(single.row = TRUE)
```
We can also see the counts
diff --git a/README.md b/README.md
index 4ec4bf2..9a738a7 100644
--- a/README.md
+++ b/README.md
@@ -152,11 +152,11 @@ simulated_Y <- sim_defm(d_model, sim_par)
head(cbind(id, simulated_Y))
#> id
#> [1,] 1 0 0 0
-#> [2,] 1 0 0 0
+#> [2,] 1 0 0 1
#> [3,] 1 0 0 0
-#> [4,] 1 0 1 1
+#> [4,] 1 1 1 1
#> [5,] 2 0 1 0
-#> [6,] 2 0 1 0
+#> [6,] 2 1 1 0
```
Now, let’s see if we can recover the parameters using MLE:
@@ -174,12 +174,12 @@ summary(ans)
#> -nobs_defm(object), 0L), lower = lower, upper = upper)
#>
#> Coefficients:
-#> Estimate Std. Error
-#> Num. of ones -1.966198 0.01401444
-#> Num. of ones x x1 1.957017 0.01548504
-#> Motif $(y0^+) -> (y0^+, y1^+)$ 4.905981 0.04516844
+#> Estimate Std. Error
+#> Num. of ones -2.009506 0.01435074
+#> Num. of ones x x1 2.020209 0.01592269
+#> Motif {y0⁺} ⇨ {y0⁺, y1⁺} 5.051076 0.04649995
#>
-#> -2 log L: 56154.07
+#> -2 log L: 54960.47
```
Or better, we can use `texreg` to generate a pretty output:
@@ -204,7 +204,7 @@ Model 1
Num. of ones
|
--1.97 (0.01)
+-2.01 (0.01)\*\*\*
|
@@ -212,16 +212,15 @@ Num. of ones
Num. of ones x x1
|
-1.96 (0.02)
+2.02 (0.02)\*\*\*
|
|
-Motif
-
+Motif {y0⁺} ⇨ {y0⁺, y1⁺}
|
-4.91 (0.05)
+5.05 (0.05)\*\*\*
|
@@ -229,7 +228,7 @@ Motif
AIC
|
-56160.07
+54966.47
|
@@ -237,7 +236,7 @@ AIC
BIC
|
-56184.76
+54991.16
|
@@ -264,14 +263,14 @@ We can also see the counts
| id | y0 | y1 | y2 | x0 | x1 | | | |
|----:|----:|----:|----:|------:|------:|----:|-----:|----:|
| 1 | 0 | 0 | 0 | 0.51 | 0.95 | NA | NA | NA |
-| 1 | 0 | 0 | 0 | 0.16 | 0.25 | 0 | 0.00 | 0 |
+| 1 | 0 | 0 | 1 | 0.16 | 0.25 | 1 | 0.25 | 0 |
| 1 | 0 | 0 | 0 | 1.20 | -1.72 | 0 | 0.00 | 0 |
-| 1 | 0 | 1 | 1 | -0.20 | 1.55 | 2 | 3.11 | 0 |
+| 1 | 1 | 1 | 1 | -0.20 | 1.55 | 3 | 4.66 | 0 |
| 2 | 0 | 1 | 0 | -0.15 | -0.68 | NA | NA | NA |
-| 2 | 0 | 1 | 0 | 1.19 | 0.92 | 1 | 0.92 | 0 |
-| 2 | 1 | 0 | 0 | -0.65 | 1.16 | 1 | 1.16 | 0 |
-| 2 | 0 | 0 | 0 | -0.99 | 0.21 | 0 | 0.00 | 0 |
-| 2 | 1 | 1 | 0 | 0.76 | 1.45 | 2 | 2.90 | 0 |
+| 2 | 1 | 1 | 0 | 1.19 | 0.92 | 2 | 1.84 | 0 |
+| 2 | 1 | 1 | 1 | -0.65 | 1.16 | 3 | 3.48 | 1 |
+| 2 | 1 | 1 | 0 | -0.99 | 0.21 | 2 | 0.43 | 1 |
+| 2 | 1 | 1 | 1 | 0.76 | 1.45 | 3 | 4.35 | 1 |
| 2 | 0 | 0 | 0 | -0.68 | -1.34 | 0 | 0.00 | 0 |
Finally, we can also take a look at the distribution of the log odds. We
@@ -400,17 +399,17 @@ d_model_formula
#> Support size : 19
#> Support size range : [11, 20]
#> Transform. Fun. : no
-#> Model terms (11) :
-#> - Motif $(y0^+, y1^-) -> (y0^-, y1^+)$
-#> - Motif $(y1^+, y2^-) -> (y1^-, y2^+)$
-#> - Motif $(y2^+, y3^-) -> (y2^-, y3^+)$
-#> - Motif $(y3^+, y4^-) -> (y3^-, y4^+)$
-#> - Motif $(y4^+, y5^-) -> (y4^-, y5^+)$
-#> - Motif $(y5^+, y6^-) -> (y5^-, y6^+)$
-#> - Motif $(y6^+, y7^-) -> (y6^-, y7^+)$
-#> - Motif $(y7^+, y8^-) -> (y7^-, y8^+)$
-#> - Motif $(y8^+, y9^-) -> (y8^-, y9^+)$
-#> - Motif $(y0^-, y9^+) -> (y0^+, y9^-)$
+#> Model terms (11) :
+#> - Motif {y0⁺, y1⁻} ⇨ {y0⁻, y1⁺}
+#> - Motif {y1⁺, y2⁻} ⇨ {y1⁻, y2⁺}
+#> - Motif {y2⁺, y3⁻} ⇨ {y2⁻, y3⁺}
+#> - Motif {y3⁺, y4⁻} ⇨ {y3⁻, y4⁺}
+#> - Motif {y4⁺, y5⁻} ⇨ {y4⁻, y5⁺}
+#> - Motif {y5⁺, y6⁻} ⇨ {y5⁻, y6⁺}
+#> - Motif {y6⁺, y7⁻} ⇨ {y6⁻, y7⁺}
+#> - Motif {y7⁺, y8⁻} ⇨ {y7⁻, y8⁺}
+#> - Motif {y8⁺, y9⁻} ⇨ {y8⁻, y9⁺}
+#> - Motif {y0⁻, y9⁺} ⇨ {y0⁺, y9⁻}
#> - Num. of ones
#> Model rules (1) :
#> - Markov model of order 1
diff --git a/man/figures/README-logodds-1.png b/man/figures/README-logodds-1.png
index 0c16134..4fab9b2 100644
Binary files a/man/figures/README-logodds-1.png and b/man/figures/README-logodds-1.png differ