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replace usethis by cli #33

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merged 2 commits into from
Jan 16, 2024
Merged

replace usethis by cli #33

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dd40c4f
replace usethis by cli
olivroy Jan 12, 2024
990e7e1
fix typo
olivroy Jan 13, 2024
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4 changes: 2 additions & 2 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
Expand Up @@ -36,10 +36,10 @@ Imports:
grDevices,
R2jags,
stats,
usethis
cli
Suggests:
knitr,
rmarkdown
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
RoxygenNote: 7.3.0
VignetteBuilder: knitr
10 changes: 5 additions & 5 deletions R/bugs-funs.R
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Original file line number Diff line number Diff line change
Expand Up @@ -701,14 +701,14 @@ diagnostic <- function(data, threshold = 1.1) {
if (length(pos)) {

no_converged <- names(bugs)[pos]

usethis::ui_oops(paste0("Some parameters have not converged for the ",
"following count series: ",
"{usethis::ui_value(no_converged)}."))
cli::cli_alert_danger(c(
"Some parameters have not converged for the following count series: ",
"{.val {no_converged}}."
))

} else {

usethis::ui_done("All models have converged.")
cli::cli_alert_success("All models have converged.")
}

invisible(NULL)
Expand Down
53 changes: 29 additions & 24 deletions R/format-funs.R
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Expand Up @@ -1118,10 +1118,10 @@ format_data <- function(data, info = NULL, date = "date", count = "count",
count_series <- count_series[-which(names(count_series) %in% series_to_del)]

if (length(n_rows) < length(count_series)) {
usethis::ui_oops(paste0("Removing the following series without valid ",
"precision measures: ",
usethis::ui_value(paste0(series_to_del,
collapse = ", "))))
cli::cli_alert_danger(c(
"Removing the following series without valid precision measures: ",
"{.val {series_to_del}}"
))
}
}

Expand All @@ -1135,10 +1135,11 @@ format_data <- function(data, info = NULL, date = "date", count = "count",

if (!na_rm) {

stop("The following count series have not enough data (< 4):\n",
usethis::ui_value(paste0(series_to_del,
collapse = ", ")),
"\nRemove these count series or use 'na_rm = TRUE'.")
cli::cli_abort(c(
"The following count series have not enough data (< 4):",
"{.val {series_to_del}}",
i = "Remove these count series or use 'na_rm = TRUE'."
))

} else {

Expand All @@ -1147,10 +1148,10 @@ format_data <- function(data, info = NULL, date = "date", count = "count",
}

if (length(n_rows) < length(count_series)) {
usethis::ui_oops(paste0("Removing the following series without enough ",
"data (< 4) ",
usethis::ui_value(paste0(series_to_del,
collapse = ", "))))
cli::cli_alert_danger(c(
"Removing the following series without enough data (< 4) ",
"{.val {series_to_del}}"
))
}
}

Expand Down Expand Up @@ -1191,10 +1192,10 @@ format_data <- function(data, info = NULL, date = "date", count = "count",
count_series <- count_series[-which(names(count_series) %in% series_to_del)]

if (length(n_rows) < length(count_series)) {
usethis::ui_oops(paste0("Removing the following series without valid ",
"precision measures: ",
usethis::ui_value(paste0(series_to_del,
collapse = ", "))))
cli::cli_alert_danger(c(
"Removing the following series without valid precision measures: ",
"{.val {series_to_del}}"
))
}
}

Expand All @@ -1209,9 +1210,10 @@ format_data <- function(data, info = NULL, date = "date", count = "count",

if (any(count_series[[i]][ , "lower_ci_conv"] ==
count_series[[i]][ , "upper_ci_conv"])) {
stop(paste0("Lower and upper CI bounds cannot be strictly equal for ",
"the series.",
usethis::ui_value(names(count_series)[i])))
cli::cli_abort(c(
"Lower and upper CI bounds cannot be strictly equal for the series.",
"{.val {names(count_series)[i]}}"
))
}
}

Expand Down Expand Up @@ -1270,9 +1272,10 @@ format_data <- function(data, info = NULL, date = "date", count = "count",
paste0(id, "_data.RData")))
}


usethis::ui_done(paste0("Detecting {usethis::ui_value(length(",
"data_series))} count series"))

cli::cli_alert_success(
"Detecting {.val {length(data_series)}} count series."
)

data_series
}
Expand Down Expand Up @@ -1302,8 +1305,10 @@ is_na_counts <- function(data, col, na_rm) {
} else {

pos <- which(is.na(data[ , col]))
usethis::ui_info(paste0("Removing {usethis::ui_value(length(pos))} ",
"rows with NA values in '", col, "' field."))

cli::cli_alert_info(c(
"Removing {.val {length(pos)}} rows with NA values in {.field {col}} field."
))

data <- data[-pos, ]
}
Expand Down
43 changes: 23 additions & 20 deletions R/series-funs.R
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Original file line number Diff line number Diff line change
Expand Up @@ -34,11 +34,12 @@ get_series <- function(data, quiet = TRUE) {
series_infos$"id" <- gsub("[[:punct:]]", "_", series_infos$"id")

if (!quiet)
usethis::ui_done(paste0("Detecting {usethis::ui_value(nrow(series_infos))}",
" series with {usethis::ui_value(length(unique(",
"series_infos$location)))} location(s) and ",
"{usethis::ui_value(length(unique(",
"series_infos$species)))} species"))

cli::cli_alert_success(c(
"Detecting {.val {nrow(series_infos)}} series with ",
"{.val {length(unique(series_infos$location))}} location{?s} and ",
"{.val {length(unique(series_infos$species))}} species."
))

series_infos
}
Expand Down Expand Up @@ -117,8 +118,9 @@ filter_series <- function(data, species = NULL, location = NULL) {

if (is.null(species) && is.null(location)) {

usethis::ui_oops(paste0("No species nor location provided to filter ",
"series."))
cli::cli_alert_danger(
"No species nor location provided to filter series"
)

return(NULL)
}
Expand Down Expand Up @@ -173,15 +175,16 @@ filter_series <- function(data, species = NULL, location = NULL) {
series_match <- which(species_detected & location_detected)

if (length(series_match)) {
usethis::ui_done(paste0("Found {usethis::ui_value(length(",
"series_match))} series with ",
"{usethis::ui_value(species)} and ",
"{usethis::ui_value(location)}."))

cli::cli_alert_success(c(
"Found {.val {length(series_match)}} series with ",
"{.val {species}} and {.val {location}}."
))
} else {

usethis::ui_oops(paste0("No series found with ",
"{usethis::ui_value(species)} and ",
"{usethis::ui_value(location)}."))
cli::cli_alert_danger(
"No series found with {.val {species}} and {.val {location}}."
)

return(NULL)
}
Expand All @@ -194,18 +197,18 @@ filter_series <- function(data, species = NULL, location = NULL) {

series_match <- species_detected

usethis::ui_done(paste0("Found {usethis::ui_value(",
"sum(species_detected))} ",
"series with {usethis::ui_value(species)}."))
cli::cli_alert_success(
"Found {.val {sum(species_detected)}} series with {.val {species}}."
)
}

if (is.null(species) && !is.null(location)) {

series_match <- location_detected

usethis::ui_done(paste0("Found {usethis::ui_value(",
"sum(location_detected))} ",
"series with {usethis::ui_value(location)}."))
cli::cli_alert_success(
"Found {.val {sum(location_detected)}} series with {.val {location}}."
)
}

data[series_match]
Expand Down
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