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Wrong header when using identity-link with GLMs #900

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Sep 11, 2023
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Wrong header when using identity-link with GLMs #900

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f4ae529
Wrong header when using identity-link with GLMs
strengejacke Sep 10, 2023
fae7e2f
prob. diff. probably better?
strengejacke Sep 10, 2023
bee2cb3
Use "Risk"
strengejacke Sep 11, 2023
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Type: Package
Package: parameters
Title: Processing of Model Parameters
Version: 0.21.1.4
Version: 0.21.1.5
Authors@R:
c(person(given = "Daniel",
family = "Lüdecke",
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3 changes: 3 additions & 0 deletions NEWS.md
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Expand Up @@ -5,6 +5,9 @@
* Fixed issue with wrong calculation of test-statistic and p-values in
`model_parameters()` for `fixest` models.

* Fixed issue with wrong column header for `glm` models with
`family = binomial("identiy")`.

* Minor fixes for `dominance_analysis()`.

# parameters 0.21.1
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12 changes: 10 additions & 2 deletions R/utils_model_parameters.R
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Expand Up @@ -16,7 +16,7 @@
wb_component = FALSE,
...) {
# capture additional arguments
dot.arguments <- list(...)

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file=R/utils_model_parameters.R,line=19,col=3,[object_name_linter] Variable and function name style should match snake_case or symbols.

# model info
info <- .safe(suppressWarnings(insight::model_info(model, verbose = FALSE)))
Expand Down Expand Up @@ -63,7 +63,7 @@
# use tryCatch, these might fail...
attr(params, "test_statistic") <- .safe(insight::find_statistic(model))
attr(params, "log_response") <- .safe(isTRUE(grepl("log", insight::find_transformation(model), fixed = TRUE)))
attr(params, "log_predictors") <- .safe(any(grepl("log", unlist(insight::find_terms(model)[c("conditional", "zero_inflated", "instruments")]), fixed = TRUE)))

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file=R/utils_model_parameters.R,line=66,col=121,[line_length_linter] Lines should not be more than 120 characters. This line is 160 characters.

# save if model is multivariate response model
if (isTRUE(info$is_multivariate)) {
Expand Down Expand Up @@ -213,16 +213,16 @@

switch(tolower(ci_method),
# abbreviations
"eti" = ,

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file=R/utils_model_parameters.R,line=216,col=5,[keyword_quote_linter] Only quote named arguments to functions if necessary, i.e., if the name is not a valid R symbol (see ?make.names).
"hdi" = ,

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file=R/utils_model_parameters.R,line=217,col=5,[keyword_quote_linter] Only quote named arguments to functions if necessary, i.e., if the name is not a valid R symbol (see ?make.names).
"si" = toupper(ci_method),

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file=R/utils_model_parameters.R,line=218,col=5,[keyword_quote_linter] Only quote named arguments to functions if necessary, i.e., if the name is not a valid R symbol (see ?make.names).
# named after people
"satterthwaite" = ,

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file=R/utils_model_parameters.R,line=220,col=5,[keyword_quote_linter] Only quote named arguments to functions if necessary, i.e., if the name is not a valid R symbol (see ?make.names).
"kenward" = ,

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file=R/utils_model_parameters.R,line=221,col=5,[keyword_quote_linter] Only quote named arguments to functions if necessary, i.e., if the name is not a valid R symbol (see ?make.names).
"wald" = insight::format_capitalize(ci_method),

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file=R/utils_model_parameters.R,line=222,col=5,[keyword_quote_linter] Only quote named arguments to functions if necessary, i.e., if the name is not a valid R symbol (see ?make.names).
# special cases
"bci" = ,

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file=R/utils_model_parameters.R,line=224,col=5,[keyword_quote_linter] Only quote named arguments to functions if necessary, i.e., if the name is not a valid R symbol (see ?make.names).
"bcai" = "BCa",

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file=R/utils_model_parameters.R,line=225,col=5,[keyword_quote_linter] Only quote named arguments to functions if necessary, i.e., if the name is not a valid R symbol (see ?make.names).
# no change otherwise
ci_method
)
Expand Down Expand Up @@ -251,7 +251,11 @@
} else if ((info$is_binomial && info$is_logit) || info$is_ordinal || info$is_multinomial || info$is_categorical) {
coef_col <- "Odds Ratio"
} else if (info$is_binomial && !info$is_logit) {
coef_col <- "Risk Ratio"
if (info$link_function == "identity") {
coef_col <- "Exp. Risk"
} else {
coef_col <- "Risk Ratio"
}
} else if (info$is_count) {
coef_col <- "IRR"
}
Expand All @@ -261,7 +265,11 @@
} else if ((info$is_binomial && info$is_logit) || info$is_ordinal || info$is_multinomial || info$is_categorical) {
coef_col <- "Log-Odds"
} else if (info$is_binomial && !info$is_logit) {
coef_col <- "Log-Risk"
if (info$link_function == "identity") {
coef_col <- "Risk"
} else {
coef_col <- "Log-Risk"
}
} else if (info$is_count) {
coef_col <- "Log-Mean"
}
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23 changes: 15 additions & 8 deletions tests/testthat/test-model_parameters.glm.R
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Expand Up @@ -3,23 +3,23 @@ skip_if_not_installed("boot")
test_that("model_parameters.lm", {
model <- lm(mpg ~ wt, data = mtcars)
params <- model_parameters(model, verbose = FALSE)
expect_equal(c(nrow(params), ncol(params)), c(2, 9))
expect_identical(c(nrow(params), ncol(params)), c(2L, 9L))
expect_equal(params$CI_high, c(41.119752761418, -4.20263490802709), tolerance = 1e-3)
expect_equal(attributes(params)$sigma, 3.045882, tolerance = 1e-3)

params <- model_parameters(model, ci = c(0.8, 0.9), verbose = FALSE)
expect_equal(c(nrow(params), ncol(params)), c(2, 10))
expect_identical(c(nrow(params), ncol(params)), c(2L, 10L))

params <- model_parameters(model, dispersion = TRUE, bootstrap = TRUE, iterations = 500, verbose = FALSE)
expect_equal(c(nrow(params), ncol(params)), c(2, 7))
expect_identical(c(nrow(params), ncol(params)), c(2L, 7L))

model <- lm(mpg ~ wt + cyl, data = mtcars)
params <- model_parameters(model, verbose = FALSE)
expect_equal(c(nrow(params), ncol(params)), c(3, 9))
expect_identical(c(nrow(params), ncol(params)), c(3L, 9L))

model <- lm(mpg ~ wt * cyl, data = mtcars)
params <- model_parameters(model, verbose = FALSE)
expect_equal(c(nrow(params), ncol(params)), c(4, 9))
expect_identical(c(nrow(params), ncol(params)), c(4L, 9L))

params <- model_parameters(model, component = "conditional", effects = "fixed", verbose = FALSE)
})
Expand All @@ -28,7 +28,7 @@ test_that("print digits model_parameters.lm", {
model <- lm(mpg ~ wt, data = mtcars)
params <- model_parameters(model, digits = 4, ci_digits = 5, verbose = FALSE)
out <- capture.output(print(params))
expect_equal(out[3], "(Intercept) | 37.2851 | 1.8776 | [33.45050, 41.11975] | 19.8576 | < .001")
expect_identical(out[3], "(Intercept) | 37.2851 | 1.8776 | [33.45050, 41.11975] | 19.8576 | < .001")
})


Expand All @@ -48,10 +48,10 @@ test_that("model_parameters.glm - binomial", {
model <- glm(vs ~ wt + cyl, data = mtcars, family = "binomial")

params <- model_parameters(model, verbose = FALSE)
expect_equal(c(nrow(params), ncol(params)), c(3, 9))
expect_identical(c(nrow(params), ncol(params)), c(3L, 9L))

params <- suppressWarnings(model_parameters(model, bootstrap = TRUE, iterations = 500, verbose = FALSE))
expect_equal(c(nrow(params), ncol(params)), c(3, 6))
expect_identical(c(nrow(params), ncol(params)), c(3L, 6L))

params <- model_parameters(model, component = "conditional", effects = "fixed", verbose = FALSE)
})
Expand All @@ -67,3 +67,10 @@ test_that("model_parameters.glm - Gamma - print", {
mp <- model_parameters(m, exponentiate = TRUE)
expect_snapshot(mp)
})

test_that("model_parameters.glm - glm, identity link", {
data(mtcars)
m <- glm(am ~ vs, data = mtcars, family = binomial(link = "identity"))
p <- model_parameters(m)
expect_identical(attributes(p)$coefficient_name, "Risk")
})
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