Skip to content

Commit

Permalink
Switch to cli dependency from crayon
Browse files Browse the repository at this point in the history
  • Loading branch information
@jacob-long
jacob-long committed Aug 1, 2024
1 parent 7374755 commit 39866e3
Show file tree
Hide file tree
Showing 5 changed files with 55 additions and 53 deletions.
4 changes: 2 additions & 2 deletions DESCRIPTION
View file
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports:
crayon,
cli,
generics,
ggplot2 (>= 3.4.0),
magrittr,
Expand Down Expand Up @@ -47,7 +47,7 @@ Enhances:
brms,
quantreg,
rstanarm
RoxygenNote: 7.2.3
RoxygenNote: 7.3.2.9000
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
Depends:
Expand Down
1 change: 1 addition & 0 deletions NAMESPACE
View file
Original file line number Diff line number Diff line change
Expand Up @@ -206,6 +206,7 @@ export(weights_tests)
export(wgttest)
export(wrap_str)
export(wtd.sd)
import(cli)
import(ggplot2)
import(rlang)
importFrom(crayon,cyan)
Expand Down
71 changes: 36 additions & 35 deletions R/summ.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,8 @@
#'
#' @export
#' @importFrom stats nobs
#'
#' @import cli
#'


summ <- function(model, ...) {
Expand Down Expand Up @@ -413,11 +414,11 @@ print.summ.lm <- function(x, ...) {
}

if (x$model.fit == TRUE && !is.null(x$modpval)) {
stats <- paste(italic("F"), "(", x$fnum, ",", x$fden, ") = ",
num_print(x$fstat, digits = x$digits), ", ", italic("p"), " = ",
stats <- paste(style_italic("F"), "(", x$fnum, ",", x$fden, ") = ",
num_print(x$fstat, digits = x$digits), ", ", style_italic("p"), " = ",
num_print(x$modpval, digits = x$digits), "\n",
italic("R\u00B2 = "), num_print(x$rsq, digits = x$digits), "\n",
italic("Adj. R\u00B2 = "), num_print(x$arsq, digits = x$digits),
style_italic("R\u00B2 = "), num_print(x$rsq, digits = x$digits), "\n",
style_italic("Adj. R\u00B2 = "), num_print(x$arsq, digits = x$digits),
sep = "")
print_mod_fit(stats)
}
Expand Down Expand Up @@ -851,9 +852,9 @@ print.summ.glm <- function(x, ...) {
type <- "Linear regression"
} else {
type <- paste("Generalized linear model\n ",
italic("Family:"),
style_italic("Family:"),
as.character(x$lmFamily[1]), "\n ",
italic("Link function:"),
style_italic("Link function:"),
as.character(x$lmFamily[2]), sep = " ")
}
print_mod_info(missing = x$missing, n = x$n, dv = x$dv, type = type)
Expand All @@ -862,13 +863,13 @@ print.summ.glm <- function(x, ...) {
if (x$model.fit == TRUE) {
stats <- paste("\u03C7\u00B2(",
x$chisq$df, ") = ", num_print(x$chisq$chi, x$digits), ", ",
italic("p"), " = ", num_print(x$chisq$p, x$digits), "\n",
italic("Pseudo-R\u00B2 (Cragg-Uhler)"), " = ",
style_italic("p"), " = ", num_print(x$chisq$p, x$digits), "\n",
style_italic("Pseudo-R\u00B2 (Cragg-Uhler)"), " = ",
num_print(x$rsq, digits = x$digits), "\n",
italic("Pseudo-R\u00B2 (McFadden)"), " = ",
style_italic("Pseudo-R\u00B2 (McFadden)"), " = ",
num_print(x$rsqmc, digits = x$digits), "\n",
italic("AIC"), " = ", num_print(x$aic, x$digits),
", ", italic("BIC"), " = ", num_print(x$bic, x$digits),
style_italic("AIC"), " = ", num_print(x$aic, x$digits),
", ", style_italic("BIC"), " = ", num_print(x$bic, x$digits),
sep = "")
print_mod_fit(stats)
}
Expand Down Expand Up @@ -1340,8 +1341,8 @@ print.summ.svyglm <- function(x, ...) {
} else {
# Otherwise just treat it like glm
type <- paste("Analysis of complex survey design", "\n",
italic("Family:"), as.character(x$lmFamily[1]),
"\n", italic("Link function:"), as.character(x$lmFamily[2]),
style_italic("Family:"), as.character(x$lmFamily[1]),
"\n", style_italic("Link function:"), as.character(x$lmFamily[2]),
sep = " ")
}
print_mod_info(missing = x$missing, n = x$n, dv = x$dv, type = type)
Expand All @@ -1351,17 +1352,17 @@ print.summ.svyglm <- function(x, ...) {
if (as.character(x$lmFamily[1]) == "gaussian" &&
as.character(x$lmFamily[2]) == "identity") {
# If it's a linear model, show regular lm fit stats
stats <- paste(italic("R\u00B2"), " = ",
stats <- paste(style_italic("R\u00B2"), " = ",
num_print(x$rsq, digits = x$digits), "\n",
italic("Adj. R\u00B2"), " = ",
style_italic("Adj. R\u00B2"), " = ",
num_print(x$arsq, digits = x$digits), sep = "")
} else {
# If it isn't linear, show GLM fit stats
stats <- paste(italic("Pseudo-R\u00B2 (Cragg-Uhler)"), " = ",
stats <- paste(style_italic("Pseudo-R\u00B2 (Cragg-Uhler)"), " = ",
num_print(x$rsq, digits = x$digits), "\n",
italic("Pseudo-R\u00B2 (McFadden)"), " = ",
style_italic("Pseudo-R\u00B2 (McFadden)"), " = ",
num_print(x$rsqmc, digits = x$digits), "\n",
italic("AIC"), " = ", num_print(x$aic, x$digits), sep = "")
style_italic("AIC"), " = ", num_print(x$aic, x$digits), sep = "")
}
print_mod_fit(stats)
}
Expand Down Expand Up @@ -2008,29 +2009,29 @@ print.summ.merMod <- function(x, ...) {
type <- "Mixed effects linear regression"
} else {
type <- paste("Mixed effects generalized linear regression", "\n",
italic("Error Distribution: "),
style_italic("Error Distribution: "),
as.character(x$lmFamily[1]), "\n",
italic("Link function: "), as.character(x$lmFamily[2]),
style_italic("Link function: "), as.character(x$lmFamily[2]),
sep = "")
}
print_mod_info(missing = x$missing, n = x$n, dv = x$dv, type = type)
}

if (x$model.fit == T) {
stats <- paste(italic("AIC"), " = ", num_print(x$aic, x$digits),
", ", italic("BIC"), " = ",
stats <- paste(style_italic("AIC"), " = ", num_print(x$aic, x$digits),
", ", style_italic("BIC"), " = ",
num_print(x$bic, x$digits), sep = "")
if (x$r.squared == TRUE) {
stats <- paste(stats, "\n", italic("Pseudo-R\u00B2 (fixed effects)"),
stats <- paste(stats, "\n", style_italic("Pseudo-R\u00B2 (fixed effects)"),
" = ", num_print(x$rsq$Marginal, x$digits), "\n",
italic("Pseudo-R\u00B2 (total)"), " = ",
style_italic("Pseudo-R\u00B2 (total)"), " = ",
num_print(x$rsq$Conditional, x$digits), sep = "")
}
print_mod_fit(stats)
}

if (x$model.coefs == TRUE) {
cat(underline("FIXED EFFECTS:\n"))
cat(style_underline("FIXED EFFECTS:\n"))
print(md_table(ctable, format = getOption("summ.table.format", "multiline"),
sig.digits = FALSE, digits = x$digits))

Expand All @@ -2039,8 +2040,8 @@ print.summ.merMod <- function(x, ...) {

if (x$p_calc == "residual") {

cat(italic$cyan("\nNote: p values calculated based on residual d.f. =",
x$df, "\n"))
cat(style_italic(col_cyan(
"\nNote: p values calculated based on residual d.f. =", x$df, "\n")))

if (is.null(x$t.df)) {
msg_wrap("Using p values with lmer based on residual d.f. may inflate
Expand All @@ -2052,26 +2053,26 @@ print.summ.merMod <- function(x, ...) {
} else if (x$p_calc %in% c("k-r", "Kenward-Roger", "kenward-roger")) {

cat("\n")
cat_wrap(italic$cyan("p values calculated using Kenward-Roger standard
errors and d.f."), brk = "\n")
cat_wrap(style_italic(col_cyan("p values calculated using Kenward-Roger
standard errors and d.f.")), brk = "\n")

} else if (x$p_calc %in% c("s", "Satterthwaite", "satterthwaite")) {

cat("\n")
cat_wrap(italic$cyan("p values calculated using Satterthwaite
d.f."), brk = "\n")
cat_wrap(style_italic(col_cyan("p values calculated using Satterthwaite
d.f.")), brk = "\n")

} else if (x$p_calc == "manual") {

cat(italic("\nNote: p values calculated based on user-defined d.f. ="),
cat(style_italic("\nNote: p values calculated based on user-defined d.f. ="),
x$df, "\n")

}

}

if (x$re.table == TRUE) {
cat(underline("\nRANDOM EFFECTS:\n"))
cat(style_underline("\nRANDOM EFFECTS:\n"))
rtable <- round_df_char(j$rcoeftable, digits = x$digits, na_vals = "")
#rownames(rtable) <- rep("", times = nrow(rtable))
# print(rtable, row.names = FALSE)
Expand All @@ -2081,7 +2082,7 @@ print.summ.merMod <- function(x, ...) {
}

if (x$groups.table == TRUE) {
cat(underline("\nGrouping variables:\n"))
cat(style_underline("\nGrouping variables:\n"))
gtable <- round_df_char(j$gvars, digits = x$digits, na_vals = "")
gtable[, "# groups"] <- as.integer(gtable[, "# groups"])
#rownames(gtable) <- rep("", times = nrow(gtable))
Expand Down
24 changes: 12 additions & 12 deletions R/summ_helpers.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -439,16 +439,16 @@ vif <- function(mod, vcov = NULL, mod.matrix = NULL, ...) {

print_mod_info <- function(missing, n, dv, type) {
if (is.null(missing) || missing == 0) {
cat(underline("MODEL INFO:"), "\n",
italic("Observations:"), " ", n, "\n",
italic("Dependent Variable:"), " ", dv, "\n", sep = "")
cat(style_underline("MODEL INFO:"), "\n",
style_italic("Observations:"), " ", n, "\n",
style_italic("Dependent Variable:"), " ", dv, "\n", sep = "")
} else {
cat(underline("MODEL INFO:"), "\n",
italic("Observations:"), " ", n, " (", missing,
cat(style_underline("MODEL INFO:"), "\n",
style_italic("Observations:"), " ", n, " (", missing,
" missing obs. deleted)", "\n",
italic("Dependent Variable:"), " ", dv, "\n", sep = "")
style_italic("Dependent Variable:"), " ", dv, "\n", sep = "")
}
cat(italic("Type:"), type, "\n\n")
cat(style_italic("Type:"), type, "\n\n")
}

## Take model info and save as list
Expand All @@ -464,7 +464,7 @@ mod_info_list <- function(missing, n, dv, type) {
## Print model fit info

print_mod_fit <- function(stats) {
cat(underline("MODEL FIT:"), "\n", sep = "")
cat(style_underline("MODEL FIT:"), "\n", sep = "")
cat(stats, "\n\n")
}

Expand All @@ -474,23 +474,23 @@ print_se_info <- function(robust, use_cluster, manual = NULL, vcov = NULL, ...)

if (identical(FALSE, robust) && is.null(vcov)) {

cat(italic("Standard errors:", ifelse(is.null(manual),
cat(style_italic("Standard errors:", ifelse(is.null(manual),
no = manual, yes = "MLE")),
"\n", sep = "")

} else if (is.null(vcov)) {

if (robust == TRUE) {robust <- "HC3"}

cat(italic("Standard errors:"), sep = "")
cat(style_italic("Standard errors:"), sep = "")

if (use_cluster == FALSE) {

cat(" Robust, ", italic("type = "), robust, "\n", sep = "")
cat(" Robust, ", style_italic("type = "), robust, "\n", sep = "")

} else if (use_cluster == TRUE) {

cat(" Cluster-robust, ", italic("type = "), robust, "\n", sep = "")
cat(" Cluster-robust, ", style_italic("type = "), robust, "\n", sep = "")

}

Expand Down
8 changes: 4 additions & 4 deletions R/summ_rq.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -249,13 +249,13 @@ print.summ.rq <- function(x, ...) {
"fnc" = "Frisch-Newton (user-specified equality constraints)")

type <- paste0("Quantile regression",
"\n ", italic("Quantile (tau): "), j$model$tau, "\n ",
italic("Method: "), method)
"\n ", style_italic("Quantile (tau): "), j$model$tau, "\n ",
style_italic("Method: "), method)
print_mod_info(missing = x$missing, n = x$n, dv = x$dv, type = type)
}

if (x$model.fit == TRUE) {
stats <- paste(italic("R\u00B9"), paste0("(", j$model$tau, ")"), " = ",
stats <- paste(style_italic("R\u00B9"), paste0("(", j$model$tau, ")"), " = ",
num_print(x$r1, digits = x$digits), sep = "")
print_mod_fit(stats)
}
Expand Down Expand Up @@ -341,7 +341,7 @@ knit_print.summ.rq <- function(x, options = NULL, ...) {
}

if (x$model.fit == T && !is.null(x$modpval)) {
stats <- paste(italic("R\u00B9"), paste0("(", j$model$tau, ")"), " = ",
stats <- paste(style_italic("R\u00B9"), paste0("(", j$model$tau, ")"), " = ",
num_print(x$r1, digits = x$digits), sep = "")
stats <- data.frame(stat = c(paste0("R\u00B9 ", "(", j$model$tau, ")")),
value = c(num_print(x$r1, digits = x$digits))
Expand Down

0 comments on commit 39866e3

Please sign in to comment.