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How the Peru checklist changed from 2025 to 2026

Source: vignettes/comparison.Rmd
comparison.Rmd

Introduction

This vignette compares the two most recent checklist objects shipped with avesperu: aves_peru_2025_v5 and aves_peru_2026_v1.

The goal is not only to show that the dataset changed, but also to answer four practical questions:

  1. How large was the update?
  2. Which status categories changed the most?
  3. Which species entered or left the checklist?
  4. Where are the changes concentrated taxonomically?

Between 29 de diciembre de 2025 and 23 de marzo de 2026, the checklist grew from 1919 to 1925 species. That is a net gain of 6 species.

At the same time, the overall structure of the database remained highly stable: 1916 species are shared by both versions, which means that 99.84% of the 2025 checklist was retained in the 2026 release.

1. High-level snapshot

The first table summarizes the scale of the update. It shows that the number of orders remained constant, while the number of family labels increased slightly.

knitr::kable(summary_tbl, caption = "High-level comparison of the two checklist versions")
High-level comparison of the two checklist versions
dataset version_date species orders families
aves_peru_2025_v5 29 de diciembre de 2025 1919 32 90
aves_peru_2026_v1 23 de marzo de 2026 1925 32 91 
summary_plot_tbl <- summary_tbl
summary_plot_tbl$release <- c("2025 v5", "2026 v1")

ggplot(summary_plot_tbl, aes(x = release, y = species, fill = release)) +
  geom_col(width = 0.62, color = NA) +
  geom_text(aes(label = species), vjust = -0.5, fontface = "bold", size = 4.2) +
  scale_fill_manual(values = c("2025 v5" = "#4C67B0", "2026 v1" = "#69B3E7")) +
  scale_y_continuous(
    expand = expansion(mult = c(0, 0.08)),
    labels = scales::comma
  ) +
  labs(
    title = "Net checklist growth between releases",
    subtitle = "The 2026 update adds 6 species relative to the 2025 release",
    x = NULL,
    y = "Number of species"
  ) +
  plot_theme +
  theme(legend.position = "none")

This graphic is useful as a first check for reproducibility: the update is not a complete restructuring of the package data, but a focused revision with a small and traceable net increase.

2. Changes in status composition

The net increase is not distributed evenly across status categories. Most of the change is concentrated in Divagante, Residente, and Endémico, while No confirmado decreases.

knitr::kable(status_tbl, caption = "Species counts by status in each dataset version")
Species counts by status in each dataset version
status n_2025 n_2026 change
Residente 1549 1552 3
Endémico 118 119 1
Migratorio 140 140 0
Divagante 86 90 4
Introducido 3 3 0
No confirmado 23 21 -2
Extirpado 0 0 0 
status_plot_tbl <- status_tbl
status_plot_tbl$direction <- ifelse(status_plot_tbl$change >= 0, "Increase", "Decrease")
status_plot_tbl$label <- ifelse(
  status_plot_tbl$change > 0,
  paste0("+", status_plot_tbl$change),
  as.character(status_plot_tbl$change)
)
status_plot_tbl$status <- factor(status_plot_tbl$status, levels = rev(status_plot_tbl$status))

ggplot(status_plot_tbl, aes(x = status, y = change, fill = direction)) +
  geom_col(width = 0.72) +
  geom_hline(yintercept = 0, linetype = 2, color = "#7A8793") +
  geom_text(
    aes(
      label = label,
      hjust = ifelse(change >= 0, -0.15, 1.15)
    ),
    size = 4
  ) +
  coord_flip() +
  scale_fill_manual(values = c("Increase" = "#4B8A5F", "Decrease" = "#B34A3C")) +
  scale_y_continuous(expand = expansion(mult = c(0.08, 0.12))) +
  labs(
    title = "Net change by status category",
    subtitle = "Vagrants and residents explain most of the checklist growth",
    x = NULL,
    y = "Change in number of species"
  ) +
  plot_theme

Three patterns stand out:

  • Divagante increases by 4 species, the largest category-level change in the update.
  • Residente increases by 3 species, showing that the revision is not restricted to occasional records.
  • No confirmado decreases by 2 species, suggesting that some previously uncertain records were either excluded or reclassified in the updated source.

3. Species turnover

The 2026 release adds 9 species and removes 3. Because the shared core remains so large, the update is best understood as a targeted revision rather than a replacement of the whole checklist.

Added species 

knitr::kable(
  added[, c("scientific_name", "english_name", "status", "family_name", "order_name")],
  caption = "Species added in aves_peru_2026_v1"
)
Species added in aves_peru_2026_v1
scientific_name english_name status family_name order_name
112 Columbina squammata Scaled Dove Divagante Columbidae Columbiformes
336 Fulica americana American Coot Divagante Rallidae Gruiformes
408 Anous stolidus Brown Noddy Divagante Laridae Charadriiformes
1360 Camptostoma sclateri Pacific Beardless-Tyrannulet Residente Camptostoma Passeriformes
1361 Camptostoma napaeum Amazonian Beardless-Tyrannulet Residente Camptostoma Passeriformes
1504 Tunchiornis ferrugineifrons Western Tawny-crowned Greenlet Residente Vireonidae Passeriformes
1595 Turdus phaeopygus Gray-flanked Thrush Residente Turdidae Passeriformes
1680 Icterus spurius Orchard Oriole Divagante Icteridae Passeriformes
1753 Sicalis columbiana Orange-fronted Yellow-Finch Residente Thraupidae Passeriformes

Removed species 

knitr::kable(
  removed[, c("scientific_name", "english_name", "status", "family_name", "order_name")],
  caption = "Species removed from the previous checklist version"
)
Species removed from the previous checklist version
scientific_name english_name status family_name order_name
1357 Camptostoma obsoletum Southern Beardless-Tyrannulet Residente Tyrannidae Passeriformes
1500 Tunchiornis ochraceiceps Tawny-crowned Greenlet Residente Vireonidae Passeriformes
1591 Turdus albicollis White-necked Thrush Residente Turdidae Passeriformes

Some of these additions and removals are especially informative. For example, the replacement of Camptostoma obsoletum by Camptostoma sclateri and Camptostoma napaeum is consistent with a taxonomic split in the source checklist. Likewise, the replacement of Tunchiornis ochraceiceps and Turdus albicollis by more specific taxa suggests an update in species limits or taxonomic circumscription.

That interpretation is an inference from the before/after pattern in the data, not an explicit annotation embedded in the dataset itself.

turnover_plot_tbl <- rbind(
  data.frame(order_name = turnover_by_order$order_name, movement = "Added", n = turnover_by_order$added),
  data.frame(order_name = turnover_by_order$order_name, movement = "Removed", n = turnover_by_order$removed)
)
turnover_plot_tbl <- turnover_plot_tbl[turnover_plot_tbl$n > 0, ]
turnover_plot_tbl$order_name <- factor(
  turnover_plot_tbl$order_name,
  levels = turnover_by_order$order_name[order(turnover_by_order$net_change, decreasing = TRUE)]
)

ggplot(turnover_plot_tbl, aes(x = order_name, y = n, fill = movement)) +
  geom_col(position = position_dodge(width = 0.72), width = 0.62) +
  geom_text(
    aes(label = n),
    position = position_dodge(width = 0.72),
    vjust = -0.45,
    size = 3.8
  ) +
  scale_fill_manual(values = c("Added" = "#69B3E7", "Removed" = "#D98C6A")) +
  scale_y_continuous(expand = expansion(mult = c(0, 0.1))) +
  labs(
    title = "Species turnover by order",
    subtitle = "Most additions and all removals occur in Passeriformes",
    x = NULL,
    y = "Number of species"
  ) +
  plot_theme +
  theme(axis.text.x = element_text(angle = 20, hjust = 1))

This plot shows that turnover is concentrated in Passeriformes, which accounts for 6 of the 9 additions and all 3 removals.

4. Where the taxonomic changes are concentrated

At a broad level, the checklist still contains 32 orders in both versions. The family layer changes more subtly, from 90 to 91 distinct family labels.

The next table isolates only the family labels whose counts changed.

knitr::kable(
  family_delta,
  caption = "Families with non-zero net change between versions"
)
Families with non-zero net change between versions
family_name n_2025 n_2026 change
89 Tyrannidae 251 250 -1
19 Columbidae 30 31 1
39 Icteridae 34 35 1
41 Laridae 30 31 1
68 Rallidae 30 31 1
81 Thraupidae 193 194 1
11 Camptostoma 0 2 2 
family_plot_tbl <- family_delta
family_plot_tbl$direction <- ifelse(family_plot_tbl$change > 0, "Increase", "Decrease")
family_plot_tbl$label <- ifelse(
  family_plot_tbl$change > 0,
  paste0("+", family_plot_tbl$change),
  as.character(family_plot_tbl$change)
)
family_plot_tbl$family_name <- factor(
  family_plot_tbl$family_name,
  levels = family_plot_tbl$family_name
)

ggplot(family_plot_tbl, aes(x = family_name, y = change, fill = direction)) +
  geom_col(width = 0.7) +
  geom_hline(yintercept = 0, linetype = 2, color = "#7A8793") +
  geom_text(
    aes(
      label = label,
      hjust = ifelse(change > 0, -0.12, 1.12)
    ),
    size = 3.8
  ) +
  coord_flip() +
  scale_fill_manual(values = c("Increase" = "#F3C94D", "Decrease" = "#C96B5C")) +
  scale_y_continuous(expand = expansion(mult = c(0.08, 0.12))) +
  labs(
    title = "Family-level concentration of checklist updates",
    subtitle = "Only a small subset of family labels changes between releases",
    x = NULL,
    y = "Net change in species count"
  ) +
  plot_theme

Two practical takeaways emerge from this comparison:

  • Most families do not change at all, which helps preserve compatibility with analyses built on the previous release.
  • The largest localized revision occurs around the Camptostoma label, while several other families gain a single species.

5. What this means for users

For most workflows, the 2026 update is a refinement rather than a disruptive schema change. The implications are straightforward:

  • If you are reproducing an analysis built with aves_peru_2025_v5, most names remain unchanged and directly comparable.
  • If your data include any of the removed species, you should re-run matching with search_avesperu() to align them with the current checklist.
  • If you work with vagrants, endemics, or recent country records, the 2026 release is especially relevant because these are the categories with the most visible shifts.

In short, aves_peru_2026_v1 preserves continuity with the previous checklist while incorporating a small but meaningful set of taxonomic and occurrence updates.