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gavinsimpson / ggvegan

ggplot-based plots for vegan
https://gavinsimpson.github.io/ggvegan/
GNU General Public License v2.0
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no functions are exportable from package #32

Closed samasafish closed 2 years ago

samasafish commented 2 years ago

Hi Gavin,

QUESTION: I love the idea of this package! After installing with the recommended remotes:: method, with no errors and loading the "ggvegan" library, no functions are available for export except "ggvegan::valid_layers()". Is there a trick I'm missing to use the functions?

Thanks for your time,

Sam

remotes::install_github("gavinsimpson/ggvegan" library(ggvegan) ggvegan::valid_layers() #only export available

sessionInfo()

R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.3.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] ggvegan_0.1-0 pairwiseAdonis_0.4 cluster_2.1.2 patchwork_1.1.1
[5] MicrobiotaProcess_1.6.3 weathermetrics_1.2.2 tidyquant_1.0.3 quantmod_0.4.18
[9] TTR_0.24.3 PerformanceAnalytics_2.0.4 xts_0.12.1 zoo_1.8-9
[13] ggtext_0.1.1 lubridate_1.8.0 wesanderson_0.3.6 viridis_0.6.2
[17] viridisLite_0.4.0 Cairo_1.5-14 cowplot_1.1.1 ggthemes_4.2.4
[21] magrittr_2.0.1 reshape_0.8.8 reshape2_1.4.4 forcats_0.5.1
[25] stringr_1.4.0 dplyr_1.0.7 purrr_0.3.4 readr_2.1.1
[29] tidyr_1.1.4 tibble_3.1.6 tidyverse_1.3.1 DivNet_0.4.0
[33] breakaway_4.7.6 DESeq2_1.34.0 SummarizedExperiment_1.24.0 Biobase_2.54.0
[37] MatrixGenerics_1.6.0 matrixStats_0.61.0 GenomicRanges_1.46.1 GenomeInfoDb_1.30.0
[41] IRanges_2.28.0 S4Vectors_0.32.3 BiocGenerics_0.40.0 metagMisc_0.0.4
[45] microbiome_1.16.0 ggplot2_3.3.5 phyloseq_1.38.0 vegan_2.5-7
[49] lattice_0.20-45 permute_0.9-5 ANCOMBC_1.4.0 corrplot_0.92
[53] pvclust_2.2-0 dendextend_1.15.2

jarioksa commented 2 years ago

There are autoplot and fortify methods among others. I suggest you check library(help=ggvegan) for a list of documentation of available functions. ggvegan defines methods for these functions and the generics (prototypes) of these functions are not exported (the generics are defined in and exported from ggplot2), but ggvegan specifies S3 methods for vegan objects.

samasafish commented 2 years ago

Ah of course, I get it now. Thanks for the quick and helpful response!