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The print method for CompadreDB objects prints the tibble contained in the @data slot. This makes sense, but recent changes to the tibble print method include suggestions to view aspects of the data that don't work on CompadreDB objects. Possible solutions:
Implement methods for viewing data that simply return the @data slot. This would mean that print(cdbobj, n = 100) would return print(cdbobj@data, n = 100) and so on for an expanded set of data-viewing functions. This seems to already be partially implemented with methods for nrow/ncol, but could be expanded to others likecolnames.
Suppress the tibble helper text when a CompadreDB object is printed. Toggling these off would involve setting option(pillar.advice = FALSE) or playing with the experimental pillar::tbl_format_footer function.
reprex
> library(Rcompadre)
> comp <- cdb_fetch("compadre")
This is COMPADRE version 6.22.5.0 (release date May_11_2022)
See user agreement at https://compadre-db.org/Help/UserAgreement
See how to cite at https://compadre-db.org/Help/HowToCite
> comp
A COM(P)ADRE database ('CompadreDB') object with 760 SPECIES and 8851 MATRICES.
# A tibble: 8,851 × 59
mat MatrixID Speci…¹ Speci…² Commo…³ Kingdom Phylum Class
<list> <int> <chr> <chr> <chr> <chr> <chr> <chr>
1 <CompdrMt> 238259 Abies_… Abies … Balsam… Plantae Pinop… Pino…
2 <CompdrMt> 238260 Abies_… Abies … Balsam… Plantae Pinop… Pino…
3 <CompdrMt> 238261 Agave_… Agave … Caribb… Plantae Magno… Lili…
4 <CompdrMt> 238262 Agave_… Agave … Caribb… Plantae Magno… Lili…
5 <CompdrMt> 238263 Allium… Allium… NA Plantae Magno… Lili…
6 <CompdrMt> 238265 Arauca… Arauca… NA Plantae Pinop… Pino…
7 <CompdrMt> 238266 Arauca… Arauca… NA Plantae Pinop… Pino…
8 <CompdrMt> 238271 Ascoph… Ascoph… NA Chroma… Heter… Phae…
9 <CompdrMt> 238272 Ascoph… Ascoph… NA Chroma… Heter… Phae…
10 <CompdrMt> 238273 Ascoph… Ascoph… NA Chroma… Heter… Phae…
# … with 8,841 more rows, 51 more variables: Order <chr>,
# Family <chr>, Genus <chr>, Species <chr>, Infraspecies <chr>,
# InfraspeciesType <chr>, OrganismType <chr>, DicotMonoc <chr>,
# AngioGymno <chr>, Authors <chr>, Journal <chr>,
# SourceType <chr>, OtherType <chr>, YearPublication <chr>,
# DOI_ISBN <chr>, AdditionalSource <chr>, StudyDuration <chr>,
# StudyStart <chr>, StudyEnd <chr>, ProjectionInterval <chr>, …
# ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names
> print(comp, n = 20)
Error in print.default(comp, n = 20) : invalid 'na.print' specification
> colnames(comp)
NULL
> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.6.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
other attached packages:
[1] Rcompadre_1.1.0
loaded via a namespace (and not attached):
[1] lattice_0.20-45 popdemo_1.3-1 fansi_1.0.3
[4] utf8_1.2.2 grid_4.2.2 lifecycle_1.0.3
[7] magrittr_2.0.3 pillar_1.8.1 rlang_1.0.6
[10] cli_3.4.1 rstudioapi_0.14 Matrix_1.5-3
[13] vctrs_0.5.1 tools_4.2.2 glue_1.6.2
[16] compiler_4.2.2 pkgconfig_2.0.3 tibble_3.1.8
[19] expm_0.999-6
The text was updated successfully, but these errors were encountered:
wpetry
changed the title
add tidy methods for CompadreDB objects or supress helper text
add methods for CompadreDB objects or supress helper text
Jan 25, 2023
wpetry
added a commit
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Jan 25, 2023
The print method for
CompadreDB
objects prints the tibble contained in the@data
slot. This makes sense, but recent changes to the tibble print method include suggestions to view aspects of the data that don't work onCompadreDB
objects. Possible solutions:@data
slot. This would mean thatprint(cdbobj, n = 100)
would returnprint(cdbobj@data, n = 100)
and so on for an expanded set of data-viewing functions. This seems to already be partially implemented with methods fornrow
/ncol
, but could be expanded to others likecolnames
.CompadreDB
object is printed. Toggling these off would involve settingoption(pillar.advice = FALSE)
or playing with the experimentalpillar::tbl_format_footer
function.reprex
The text was updated successfully, but these errors were encountered: