Dependency analysis on package phyr

General information

CRAN link link
Package version1.1.0
Number of strong dependencies65
Number of all dependencies179
Number of parent packages14
Max heaviness from parent packages6
Total heaviness from parent packages17
Number of parent packages (including Suggests and Enhances)29
Max co-heaviness from parent packages ("lme4" and "nloptr")18

Dependency heatmap

In the following dependency heatmap, rows are the parent packages of phyr and columns are the dependency packages that each parent package brings in. On the right side of the heatmap, there are three barplot annotations: 1. number of imported functions/S4 methods/S4 classes from parent packages; 2. number of dependency packages from each parent package; 3. heaviness of each parent package on phyr.

Adjust heatmap size:
Base packages Other packages Imports LinkingTo Suggests utils methods stats grDevices graphics grid tools parallel splines lattice magrittr glue R6 nlme Rcpp rlang pkgconfig crayon digest lifecycle tibble vctrs pillar ellipsis fansi cli utf8 withr Matrix MASS evaluate jsonlite gtable RColorBrewer brio callr desc pkgload praise processx ps waldo rprojroot rstudioapi diffobj rematch2 generics tidyselect purrr testthat dplyr cpp11 boot minqa nloptr RcppEigen png jpeg ape mgcv yaml isoband scales farver labeling munsell viridisLite colorspace stringr stringi codetools curl ggplot2 highr xfun coda vegan permute cluster future.apply future globals listenv parallelly httr lazyeval mime openssl askpass sys bslib htmltools jquerylib sass base64enc fastmap fs rappdirs plyr tidyr lme4 corpcor tensorA cubature rex knitr tinytex mice formula.tools broom operator.tools backports caper picante quantreg mvtnorm ade4 FD animation phytools SparseM MatrixModels survival pixmap sp geometry magick maps clusterGeneration combinat expm mnormt numDeriv phangorn plotrix scatterplot3d magic lpSolve linprog RcppProgress fastmatch igraph quadprog abind phylolm gap lmtest qgam gap.datasets plotly zoo shiny doParallel htmlwidgets crosstalk data.table promises httpuv xtable fontawesome sourcetools later commonmark cachem foreach iterators 0 5 10 Imported methods 0 50 100 Required packages 0 20 40 Heaviness from parents stats methods graphics Rcpp mvtnorm gridExtra Matrix latticeExtra ape dplyr tidyr nloptr lme4 RcppArmadillo rbenchmark INLA knitr MCMCglmm picante phylolm covr rmarkdown testthat ggplot2 ggridges logistf pez rr2 DHARMa In total 65 packages are required directly or indirectly (179) when installing 'phyr' (1.1.0) Imports LinkingTo Suggests Base packages that are required Recommended packages that are required Contributed packages that are required Packages that are required for installing 'phyr' Imported functions Imported S4 methods Imported S4 classes The whole namespace is imported Package is listed in 'Imports' but namespace is not imported


Dependency table

"Import" information is from the NAMESPACE file of phyr.

imports: number of imported functions/objects; importMethods: number of imported S4 methods; importClasses: number of imported S4 classes.

Required packages: number of strong dependency packages for each of the parent package (or in other words, number of dependency packages the parent package brings in).

Heaviness from parent on phyr: number of required packages that can be reduced if moving parent package to Suggests of phyr.

Parent package Field imports importMethods importClasses Required packages Heaviness from parent on phyr
lme4 Imports 2 0 0 49 6
latticeExtra Imports Parent package is listed in Imports of phyr but no object from parent package is imported. 9 4
gridExtra Imports Parent package is listed in Imports of phyr but no object from parent package is imported. 5 2
tidyr Imports Parent package is listed in Imports of phyr but no object from parent package is imported. 22 2
mvtnorm Imports Parent package is listed in Imports of phyr but no object from parent package is imported. 2 1
ape Imports 7 0 0 11 1
stats Imports The whole set of functions/methods/classes from parent package is imported to the namespace of phyr. 0 0
methods Imports 4 0 0 0 0
graphics Imports 2 0 0 0 0
Rcpp Imports 1 0 0 2 0
Matrix Imports 0 8 3 7 0
dplyr Imports 1 0 0 20 0
nloptr Imports Parent package is listed in Imports of phyr but no object from parent package is imported. 37 0
RcppArmadillo LinkingTo Parent package is listed in LinkingTo of phyr but no object from parent package is imported. 4 1
DHARMa Suggests No object is imported into the namespace of phyr. 107 49
pez Suggests No object is imported into the namespace of phyr. 55 38
logistf Suggests No object is imported into the namespace of phyr. 53 17
rmarkdown Suggests No object is imported into the namespace of phyr. 27 16
ggridges Suggests No object is imported into the namespace of phyr. 40 11
covr Suggests No object is imported into the namespace of phyr. 20 10
ggplot2 Suggests No object is imported into the namespace of phyr. 37 9
rr2 Suggests No object is imported into the namespace of phyr. 58 8
phylolm Suggests No object is imported into the namespace of phyr. 19 7
knitr Suggests No object is imported into the namespace of phyr. 12 6
MCMCglmm Suggests No object is imported into the namespace of phyr. 17 5
picante Suggests No object is imported into the namespace of phyr. 19 5
rbenchmark Suggests No object is imported into the namespace of phyr. 0 1
INLA Suggests No object is imported into the namespace of phyr. 0 1
testthat Suggests No object is imported into the namespace of phyr. 36 0

The following table lists pairs of parent packages with co-heaviness larger than 10. The co-heaviness measures the number of additional dependencies that two parent packages simultaneously import and are only imported by the two parents.

Note the co-heaviness from parents can be always easily observed in the dependency heatmap.

Parent 1 Parent 2 Co-heaviness on phyr Co-heaviness as Jaccard coeffcient
nloptr lme4 18 0.75

Analysis was done with pkgndep.