nichevol
Tools for Ecological Niche Evolution Assessment Considering Uncertainty
v0.1.20
·
Mar 10, 2023
·
GPL-3
Description
A collection of tools that allow users to perform critical steps in the process of assessing ecological niche evolution over phylogenies, with uncertainty incorporated explicitly in reconstructions. The method proposed here for ancestral reconstruction of ecological niches characterizes species' niches using a bin-based approach that incorporates uncertainty in estimations. Compared to other existing methods, the approaches presented here reduce risk of overestimation of amounts and rates of ecological niche evolution. The main analyses include: initial exploration of environmental data in occurrence records and accessible areas, preparation of data for phylogenetic analyses, executing comparative phylogenetic analyses of ecological niches, and plotting for interpretations. Details on the theoretical background and methods used can be found in: Owens et al. (2020) <doi:10.1002/ece3.6359>, Peterson et al. (1999) <doi:10.1126/science.285.5431.1265>, Soberón and Peterson (2005) <doi:10.17161/bi.v2i0.4>, Peterson (2011) <doi:10.1111/j.1365-2699.2010.02456.x>, Barve et al. (2011) <doi:10.1111/ecog.02671>, Machado-Stredel et al. (2021) <doi:10.21425/F5FBG48814>, Owens et al. (2013) <doi:10.1016/j.ecolmodel.2013.04.011>, Saupe et al. (2018) <doi:10.1093/sysbio/syx084>, and Cobos et al. (2021) <doi:10.1111/jav.02868>.
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CRAN Check Status
13
NOTE
Show all 13 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | NOTE |
| r-devel-linux-x86_64-debian-gcc | NOTE |
| r-devel-linux-x86_64-fedora-clang | NOTE |
| r-devel-linux-x86_64-fedora-gcc | NOTE |
| r-devel-windows-x86_64 | NOTE |
| r-oldrel-macos-arm64 | NOTE |
| r-oldrel-macos-x86_64 | NOTE |
| r-oldrel-windows-x86_64 | NOTE |
| r-patched-linux-x86_64 | NOTE |
| r-release-linux-x86_64 | NOTE |
| r-release-macos-arm64 | NOTE |
| r-release-macos-x86_64 | NOTE |
| r-release-windows-x86_64 | NOTE |
Check details (13 non-OK)
NOTE
r-devel-linux-x86_64-debian-clang
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol_bars.Rd:81: Lost braces; missing escapes or markup?
81 | \item if (ancestor == present & descendant == present) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_bars.Rd:82: Lost braces; missing escapes or markup?
82 | \item if (ancestor == present & descendant == unknown) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_bars.Rd:83: Lost braces; missing escapes or markup?
83 | \item if (ancestor == absent & descendant == present) {change <- "expansion"}
| ^
checkRd: (-1) nichevol_bars.Rd:84: Lost braces; missing escapes or markup?
84 | \it
...[truncated]...
<- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:75: Lost braces; missing escapes or markup?
75 | \item if (ancestor == absent & descendant == unknown) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:76: Lost braces; missing escapes or markup?
76 | \item if (ancestor == unknown & descendant == absent) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:77: Lost braces; missing escapes or markup?
77 | \item if (ancestor == unknown & descendant == present) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-devel-linux-x86_64-debian-gcc
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol_bars.Rd:81: Lost braces; missing escapes or markup?
81 | \item if (ancestor == present & descendant == present) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_bars.Rd:82: Lost braces; missing escapes or markup?
82 | \item if (ancestor == present & descendant == unknown) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_bars.Rd:83: Lost braces; missing escapes or markup?
83 | \item if (ancestor == absent & descendant == present) {change <- "expansion"}
| ^
checkRd: (-1) nichevol_bars.Rd:84: Lost braces; missing escapes or markup?
84 | \it
...[truncated]...
<- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:75: Lost braces; missing escapes or markup?
75 | \item if (ancestor == absent & descendant == unknown) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:76: Lost braces; missing escapes or markup?
76 | \item if (ancestor == unknown & descendant == absent) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:77: Lost braces; missing escapes or markup?
77 | \item if (ancestor == unknown & descendant == present) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-devel-linux-x86_64-fedora-clang
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol_bars.Rd:81: Lost braces; missing escapes or markup?
81 | \item if (ancestor == present & descendant == present) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_bars.Rd:82: Lost braces; missing escapes or markup?
82 | \item if (ancestor == present & descendant == unknown) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_bars.Rd:83: Lost braces; missing escapes or markup?
83 | \item if (ancestor == absent & descendant == present) {change <- "expansion"}
| ^
checkRd: (-1) nichevol_bars.Rd:84: Lost braces; missing escapes or markup?
84 | \it
...[truncated]...
<- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:75: Lost braces; missing escapes or markup?
75 | \item if (ancestor == absent & descendant == unknown) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:76: Lost braces; missing escapes or markup?
76 | \item if (ancestor == unknown & descendant == absent) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:77: Lost braces; missing escapes or markup?
77 | \item if (ancestor == unknown & descendant == present) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-devel-linux-x86_64-fedora-gcc
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol_bars.Rd:81: Lost braces; missing escapes or markup?
81 | \item if (ancestor == present & descendant == present) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_bars.Rd:82: Lost braces; missing escapes or markup?
82 | \item if (ancestor == present & descendant == unknown) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_bars.Rd:83: Lost braces; missing escapes or markup?
83 | \item if (ancestor == absent & descendant == present) {change <- "expansion"}
| ^
checkRd: (-1) nichevol_bars.Rd:84: Lost braces; missing escapes or markup?
84 | \it
...[truncated]...
<- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:75: Lost braces; missing escapes or markup?
75 | \item if (ancestor == absent & descendant == unknown) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:76: Lost braces; missing escapes or markup?
76 | \item if (ancestor == unknown & descendant == absent) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:77: Lost braces; missing escapes or markup?
77 | \item if (ancestor == unknown & descendant == present) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-devel-windows-x86_64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol_bars.Rd:81: Lost braces; missing escapes or markup?
81 | \item if (ancestor == present & descendant == present) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_bars.Rd:82: Lost braces; missing escapes or markup?
82 | \item if (ancestor == present & descendant == unknown) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_bars.Rd:83: Lost braces; missing escapes or markup?
83 | \item if (ancestor == absent & descendant == present) {change <- "expansion"}
| ^
checkRd: (-1) nichevol_bars.Rd:84: Lost braces; missing escapes or markup?
84 | \it
...[truncated]...
<- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:75: Lost braces; missing escapes or markup?
75 | \item if (ancestor == absent & descendant == unknown) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:76: Lost braces; missing escapes or markup?
76 | \item if (ancestor == unknown & descendant == absent) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:77: Lost braces; missing escapes or markup?
77 | \item if (ancestor == unknown & descendant == present) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-oldrel-macos-arm64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol_bars.Rd:81: Lost braces; missing escapes or markup?
81 | \item if (ancestor == present & descendant == present) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_bars.Rd:82: Lost braces; missing escapes or markup?
82 | \item if (ancestor == present & descendant == unknown) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_bars.Rd:83: Lost braces; missing escapes or markup?
83 | \item if (ancestor == absent & descendant == present) {change <- "expansion"}
| ^
checkRd: (-1) nichevol_bars.Rd:84: Lost braces; missing escapes or markup?
84 | \it
...[truncated]...
<- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:75: Lost braces; missing escapes or markup?
75 | \item if (ancestor == absent & descendant == unknown) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:76: Lost braces; missing escapes or markup?
76 | \item if (ancestor == unknown & descendant == absent) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:77: Lost braces; missing escapes or markup?
77 | \item if (ancestor == unknown & descendant == present) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-oldrel-macos-x86_64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol_bars.Rd:81: Lost braces; missing escapes or markup?
81 | \item if (ancestor == present & descendant == present) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_bars.Rd:82: Lost braces; missing escapes or markup?
82 | \item if (ancestor == present & descendant == unknown) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_bars.Rd:83: Lost braces; missing escapes or markup?
83 | \item if (ancestor == absent & descendant == present) {change <- "expansion"}
| ^
checkRd: (-1) nichevol_bars.Rd:84: Lost braces; missing escapes or markup?
84 | \it
...[truncated]...
<- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:75: Lost braces; missing escapes or markup?
75 | \item if (ancestor == absent & descendant == unknown) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:76: Lost braces; missing escapes or markup?
76 | \item if (ancestor == unknown & descendant == absent) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:77: Lost braces; missing escapes or markup?
77 | \item if (ancestor == unknown & descendant == present) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-oldrel-windows-x86_64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol_bars.Rd:81: Lost braces; missing escapes or markup?
81 | \item if (ancestor == present & descendant == present) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_bars.Rd:82: Lost braces; missing escapes or markup?
82 | \item if (ancestor == present & descendant == unknown) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_bars.Rd:83: Lost braces; missing escapes or markup?
83 | \item if (ancestor == absent & descendant == present) {change <- "expansion"}
| ^
checkRd: (-1) nichevol_bars.Rd:84: Lost braces; missing escapes or markup?
84 | \it
...[truncated]...
<- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:75: Lost braces; missing escapes or markup?
75 | \item if (ancestor == absent & descendant == unknown) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:76: Lost braces; missing escapes or markup?
76 | \item if (ancestor == unknown & descendant == absent) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:77: Lost braces; missing escapes or markup?
77 | \item if (ancestor == unknown & descendant == present) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-patched-linux-x86_64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol_bars.Rd:81: Lost braces; missing escapes or markup?
81 | \item if (ancestor == present & descendant == present) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_bars.Rd:82: Lost braces; missing escapes or markup?
82 | \item if (ancestor == present & descendant == unknown) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_bars.Rd:83: Lost braces; missing escapes or markup?
83 | \item if (ancestor == absent & descendant == present) {change <- "expansion"}
| ^
checkRd: (-1) nichevol_bars.Rd:84: Lost braces; missing escapes or markup?
84 | \it
...[truncated]...
<- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:75: Lost braces; missing escapes or markup?
75 | \item if (ancestor == absent & descendant == unknown) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:76: Lost braces; missing escapes or markup?
76 | \item if (ancestor == unknown & descendant == absent) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:77: Lost braces; missing escapes or markup?
77 | \item if (ancestor == unknown & descendant == present) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-release-linux-x86_64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol_bars.Rd:81: Lost braces; missing escapes or markup?
81 | \item if (ancestor == present & descendant == present) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_bars.Rd:82: Lost braces; missing escapes or markup?
82 | \item if (ancestor == present & descendant == unknown) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_bars.Rd:83: Lost braces; missing escapes or markup?
83 | \item if (ancestor == absent & descendant == present) {change <- "expansion"}
| ^
checkRd: (-1) nichevol_bars.Rd:84: Lost braces; missing escapes or markup?
84 | \it
...[truncated]...
<- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:75: Lost braces; missing escapes or markup?
75 | \item if (ancestor == absent & descendant == unknown) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:76: Lost braces; missing escapes or markup?
76 | \item if (ancestor == unknown & descendant == absent) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:77: Lost braces; missing escapes or markup?
77 | \item if (ancestor == unknown & descendant == present) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-release-macos-arm64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol_bars.Rd:81: Lost braces; missing escapes or markup?
81 | \item if (ancestor == present & descendant == present) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_bars.Rd:82: Lost braces; missing escapes or markup?
82 | \item if (ancestor == present & descendant == unknown) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_bars.Rd:83: Lost braces; missing escapes or markup?
83 | \item if (ancestor == absent & descendant == present) {change <- "expansion"}
| ^
checkRd: (-1) nichevol_bars.Rd:84: Lost braces; missing escapes or markup?
84 | \it
...[truncated]...
<- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:75: Lost braces; missing escapes or markup?
75 | \item if (ancestor == absent & descendant == unknown) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:76: Lost braces; missing escapes or markup?
76 | \item if (ancestor == unknown & descendant == absent) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:77: Lost braces; missing escapes or markup?
77 | \item if (ancestor == unknown & descendant == present) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-release-macos-x86_64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol_bars.Rd:81: Lost braces; missing escapes or markup?
81 | \item if (ancestor == present & descendant == present) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_bars.Rd:82: Lost braces; missing escapes or markup?
82 | \item if (ancestor == present & descendant == unknown) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_bars.Rd:83: Lost braces; missing escapes or markup?
83 | \item if (ancestor == absent & descendant == present) {change <- "expansion"}
| ^
checkRd: (-1) nichevol_bars.Rd:84: Lost braces; missing escapes or markup?
84 | \it
...[truncated]...
<- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:75: Lost braces; missing escapes or markup?
75 | \item if (ancestor == absent & descendant == unknown) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:76: Lost braces; missing escapes or markup?
76 | \item if (ancestor == unknown & descendant == absent) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:77: Lost braces; missing escapes or markup?
77 | \item if (ancestor == unknown & descendant == present) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-release-windows-x86_64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol_bars.Rd:81: Lost braces; missing escapes or markup?
81 | \item if (ancestor == present & descendant == present) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_bars.Rd:82: Lost braces; missing escapes or markup?
82 | \item if (ancestor == present & descendant == unknown) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_bars.Rd:83: Lost braces; missing escapes or markup?
83 | \item if (ancestor == absent & descendant == present) {change <- "expansion"}
| ^
checkRd: (-1) nichevol_bars.Rd:84: Lost braces; missing escapes or markup?
84 | \it
...[truncated]...
<- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:75: Lost braces; missing escapes or markup?
75 | \item if (ancestor == absent & descendant == unknown) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:76: Lost braces; missing escapes or markup?
76 | \item if (ancestor == unknown & descendant == absent) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:77: Lost braces; missing escapes or markup?
77 | \item if (ancestor == unknown & descendant == present) {change <- "no_change"}
| ^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
Check History
NOTE 0 OK · 13 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 9, 2026
NOTE
r-devel-linux-x86_64-debian-clang
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-devel-linux-x86_64-debian-gcc
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-devel-linux-x86_64-fedora-clang
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-devel-linux-x86_64-fedora-gcc
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-devel-windows-x86_64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-patched-linux-x86_64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-release-linux-x86_64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-release-macos-arm64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-release-macos-x86_64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-release-windows-x86_64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-oldrel-macos-arm64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-oldrel-macos-x86_64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-oldrel-windows-x86_64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
ERROR 0 OK · 12 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jun 8, 2026
NOTE
r-devel-linux-x86_64-debian-clang
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
ERROR
r-devel-linux-x86_64-debian-gcc
package dependencies
Package required but not available: ‘geiger’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
NOTE
r-devel-linux-x86_64-fedora-clang
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-devel-linux-x86_64-fedora-gcc
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-devel-windows-x86_64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-patched-linux-x86_64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-release-linux-x86_64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-release-macos-arm64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-release-macos-x86_64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-release-windows-x86_64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-oldrel-macos-arm64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-oldrel-macos-x86_64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-oldrel-windows-x86_64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE 0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
NOTE
r-devel-linux-x86_64-debian-clang
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-devel-linux-x86_64-debian-gcc
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-devel-linux-x86_64-fedora-clang
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-devel-linux-x86_64-fedora-gcc
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-devel-macos-arm64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-devel-windows-x86_64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-patched-linux-x86_64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-release-linux-x86_64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-release-macos-arm64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-release-macos-x86_64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-release-windows-x86_64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-oldrel-macos-arm64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-oldrel-macos-x86_64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^
NOTE
r-oldrel-windows-x86_64
Rd files
checkRd: (-1) nichevol_bars.Rd:80: Lost braces; missing escapes or markup?
80 | \item if (ancestor == present & descendant == absent) {change <- "retraction"}
| ^
checkRd: (-1) nichevol
...[truncated]...
^
checkRd: (-1) nichevol_labels.Rd:78: Lost braces; missing escapes or markup?
78 | \item if (ancestor == unknown & descendant == unknown) {change <- "no_change"}
| ^