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Compute Dominance levels from input data #152

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Merged
sbuis merged 2 commits into from
Feb 26, 2026
Merged

Compute Dominance levels from input data #152

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e4b6447
feat(dominance): compute Dominance levels from input data instead of …
sbuis Feb 26, 2026
228e853
fix: preserve factor levels when converting Dominance columns
sbuis Feb 26, 2026
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22 changes: 13 additions & 9 deletions R/cropr_formatting.R
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Original file line number Diff line number Diff line change
Expand Up @@ -102,10 +102,12 @@ format_cropr <- function(sim, obs = NULL, obs_sd = NULL,

# Treating Dominance as a factor if any (for plotting reasons):
if (is_mixture_sim) {
sim$Dominance <- factor(
sim$Dominance,
levels = c("Principal", "Associated")
)
if (!is.factor(sim$Dominance)) {
sim$Dominance <- factor(
sim$Dominance,
levels = unique(sim$Dominance)
)
}
}

# Check variable names:
Expand Down Expand Up @@ -173,12 +175,14 @@ format_cropr <- function(sim, obs = NULL, obs_sd = NULL,
obs_sd <- dplyr::full_join(obs_sd, corresp_table, by = "Plant")
}
} else {
obs$Dominance <- factor(obs$Dominance,
levels = c("Principal", "Associated")
)
if (is_obs_sd) {
if (!is.factor(obs$Dominance)) {
obs$Dominance <- factor(obs$Dominance,
levels = unique(obs$Dominance)
)
}
if (is_obs_sd & !is.factor(obs_sd$Dominance)) {
obs_sd$Dominance <- factor(obs_sd$Dominance,
levels = c("Principal", "Associated")
levels = unique(obs_sd$Dominance)
)
}
}
Expand Down
6 changes: 4 additions & 2 deletions R/generic_formatting.R
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Expand Up @@ -37,8 +37,10 @@ generic_formatting <- function(
# Replace NAs with "Single-crop" in Dominance in order to make
# the legend understandable
if ("Dominance" %in% colnames(df)) {
levels(df$Dominance) <- c("Principal", "Associated", "Single crop")
df$Dominance[which(is.na(df$Dominance))] <- "Single crop"
if ((!"Single crop" %in% levels(df$Dominance)) & any(is.na(df$Dominance))) {
levels(df$Dominance) <- c(levels(df$Dominance), "Single crop")
df$Dominance[is.na(df$Dominance)] <- "Single crop"
}
}

# Add group_var column to data frame if overlap != null
Expand Down
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