pr2database
The protist reference database keeps widening past the rRNA gene it was built on.
Comparison · Infra & APIs
mmpca vs valr
A side-by-side editorial comparison of mmpca and valr — release velocity, themes, recent moves, and the top alternatives to consider.
mmpca vs valr: at a glance
What is mmpca?
Back from CRAN removal under a new maintainer, with the compiled layer rebuilt.
mmpca implements multiple matrix principal component analysis with a compiled GSL backend. The package spent time off CRAN, and its recent history is a rescue operation rather than a feature program: a new maintainer took it over, moved the native build path onto RcppGSL, and folded the hand-written C bindings into Rcpp. The two most recent entries landed the same day, one restoring the package and one clearing residual CRAN comments.
What is valr?
valr's interval verbs now read genomic files in place instead of demanding a loaded tibble.
valr reimplements bedtools-style genome interval arithmetic as tidyverse verbs backed by C++. Its long project has been closing the behavioural gap with bedtools — the book-ended interval semantics finally match in 0.10.0, three releases after the deprecation began. The July release also ends the assumption that intervals must be in memory: bed_map(), bed_intersect(), bed_subtract(), bed_coverage() and bed_window() accept a bigWig or bigBed path or URL where an interval table used to go.
mmpca vs valr: editorial side-by-side
mmpca
0.0INFRA · APIS
Back from CRAN removal under a new maintainer, with the compiled layer rebuilt.
◆ Current state
mmpca implements multiple matrix principal component analysis with a compiled GSL backend. The package spent time off CRAN, and its recent history is a rescue operation rather than a feature program: a new maintainer took it over, moved the native build path onto RcppGSL, and folded the hand-written C bindings into Rcpp. The two most recent entries landed the same day, one restoring the package and one clearing residual CRAN comments.
◆ Where it's heading
Work is concentrated on making the package installable and check-clean rather than on the decomposition itself. The version stamps run out of order, with 2.0.3 predating both 2.0.2 and 2.0.4 by three years, so the feed reads as an archive flush around the CRAN return. Nothing in the entries points at method-level work.
◆ Prediction
Expect maintenance releases that keep the compiled code passing CRAN checks; the entries give no signal about new decomposition features.
valr
0.0INFRA · APIS
valr's interval verbs now read genomic files in place instead of demanding a loaded tibble.
◆ Current state
valr reimplements bedtools-style genome interval arithmetic as tidyverse verbs backed by C++. Its long project has been closing the behavioural gap with bedtools — the book-ended interval semantics finally match in 0.10.0, three releases after the deprecation began. The July release also ends the assumption that intervals must be in memory: bed_map(), bed_intersect(), bed_subtract(), bed_coverage() and bed_window() accept a bigWig or bigBed path or URL where an interval table used to go.
◆ Where it's heading
Two arcs converge here. One is compatibility: min_overlap arrived with a deprecation warning in 0.9.0 and its default flipped from 0 to 1 in 0.10.0, so book-ended intervals are excluded by default as bedtools does, with the internal calculations in bed_closest() and friends deliberately left counting them. The other is the file-backed path, which grew out of the cpp11bigwig dependency adopted in 0.8.3 for read_bigwig() and re-exported in 0.9.0 — reading a file became querying one. Underneath, the C++ base keeps getting lighter: Rcpp swapped for cpp11, rlang cut to a single function, per-group memory copies removed from three verbs.
◆ Prediction
Only five verbs take a file argument today and bed_closest(), bed_glyph() and the statistical verbs do not, so extending the file-backed path across the rest of the API is the obvious follow-up. The deprecated tibble re-exports and the now-defunct n_fields argument suggest continued removal of the compatibility layer in the next minor release.
Alternatives to mmpca and valr
Other Infra & APIs products tracked by Sparkpulse, ranked by recent ship velocity. Each card links to a full editorial trajectory and lets you pivot into a head-to-head comparison with either mmpca or valr.
ggalign
Composable aligned layouts, rebuilt on S7 while ggplot2 4.0 lands underneath.
prioritizr
Conservation planning absorbs the literature's target-setting rules as code.
jSDM
Joint species distribution models in Gibbs-sampled C++, quiet since 2023.
rsofun
An ecosystem model starts tracking carbon isotopes and land-use change.
usmap
Ten years in, US mapping splits its data out and finally adds Puerto Rico.
Recent activity from mmpca and valr
Latest ship moves from both products, interleaved chronologically. ⚡ = editorial spark.
- 1mo agovalrInterval verbs read bigWig and bigBed files directly ⚡
- 7mo agovalrbed_slop() and bed_flank() preserve input row order
- 8mo agommpcaMinor CRAN comments cleared to keep the package listed
- 8mo agommpcaBack on CRAN under a new maintainer, rebuilt on RcppGSL ⚡
- 8mo agovalrmin_overlap introduced; C++ backend moves from Rcpp to cpp11
- 1y agovalrTest updated for ggplot2 3.6.0
- 1y agovalrread_bigwig() switches to cpp11bigwig; read_gtf() deprecated
- 1y agovalrCRAN Rd link NOTE and maintainer email change
- 3y agommpcaValgrind memory fixes and a maximum-iteration option
Frequently asked questions
What is the difference between mmpca and valr?
They serve adjacent needs but don't currently overlap on shipped themes. mmpca and valr are shipping at a similar cadence (velocity 0.0 vs 0.0, both within Sparkpulse's "active" band). See the at-a-glance table above for a side-by-side breakdown of velocity, recent sparks, and editorial themes.
Is mmpca better than valr?
Sparkpulse doesn't pick a winner — we score release velocity, not feature parity. mmpca and valr are shipping at a similar cadence (velocity 0.0 vs 0.0, both within Sparkpulse's "active" band). For your specific use case, the alternatives sections above list other Infra & APIs products to evaluate alongside.
What are the best alternatives to mmpca?
Top mmpca alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "mmpca alternatives" section above for the current picks, or visit /alternatives/mmpca for the full list with editorial commentary on each.
What are the best alternatives to valr?
Top valr alternatives in Infra & APIs are ranked by recent ship velocity. Browse the "valr alternatives" section above for the current picks, or visit /alternatives/valr for the full list with editorial commentary on each.