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JOSS submission and dplyr fix.#85

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sdhutchins merged 64 commits intodev-masterfrom
joss-branch2
Feb 27, 2019
Merged

JOSS submission and dplyr fix.#85
sdhutchins merged 64 commits intodev-masterfrom
joss-branch2

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@grabear grabear commented Feb 27, 2019

MicrobiomeR 0.5.1

MicrobiomeR 0.5.0

  • Added the JOSS paper and draft vignette
  • Changed correlation plots
    • Removed color from background
    • Removed hard coded plot limits
    • Added "1:1" line and Average lines
    • Added a trans parameter to transform the x and y axis
  • Changed function names
    • From create_metacoder to create_taxmap
    • From agglomerate_metacoder to agglomerate_taxmap
    • From melt_metacoder to melt_taxmap
  • Bugs
    • Fixed output_dir bug where error should have been a warning
    • Fixed correlation plot bug where treatments were on the wrong axis.
    • Fixed output message for heat tree plots.
  • Fixed build-check Notes and Warnings

grabear and others added 30 commits January 24, 2019 12:50
# Conflicts:
#	DESCRIPTION
#	NAMESPACE
#	NEWS.md
#	R/alpha-diversity.R
#	R/barplot.R
#	docs/CODE_OF_CONDUCT.html
#	docs/CONTRIBUTING.html
#	docs/ISSUE_TEMPLATE.html
#	docs/LICENSE-text.html
#	docs/PULL_REQUEST_TEMPLATE.html
#	docs/articles/about.html
#	docs/articles/analysis.html
#	docs/articles/analysis_files/figure-html/unnamed-chunk-7-1.png
#	docs/articles/analysis_files/figure-html/unnamed-chunk-7-2.png
#	docs/articles/analysis_files/figure-html/unnamed-chunk-7-3.png
#	docs/articles/analysis_files/figure-html/unnamed-chunk-8-1.png
#	docs/articles/analysis_files/figure-html/unnamed-chunk-8-2.png
#	docs/articles/analysis_files/figure-html/unnamed-chunk-8-3.png
#	docs/articles/analysis_files/figure-html/unnamed-chunk-9-1.png
#	docs/articles/analysis_files/figure-html/unnamed-chunk-9-2.png
#	docs/articles/analysis_files/figure-html/unnamed-chunk-9-3.png
#	docs/articles/analysis_files/figure-html/unnamed-chunk-9-4.png
#	docs/articles/analysis_files/figure-html/unnamed-chunk-9-5.png
#	docs/articles/analysis_files/figure-html/unnamed-chunk-9-6.png
#	docs/articles/color-palettes.html
#	docs/articles/data-wrangling.html
#	docs/articles/filtering.html
#	docs/articles/index.html
#	docs/articles/introduction.html
#	docs/authors.html
#	docs/index.html
#	docs/news/index.html
#	docs/reference/MicrobiomeR.html
#	docs/reference/MicrobiomeR_Formats.html
#	docs/reference/MicrobiomeR_Workflow.html
#	docs/reference/alpha_diversity_plot.html
#	docs/reference/as_MicrobiomeR_format.html
#	docs/reference/as_analyzed_format.html
#	docs/reference/as_basic_format.html
#	docs/reference/as_custom_format.html
#	docs/reference/as_phyloseq_format.html
#	docs/reference/as_raw_format.html
#	docs/reference/combination_palette.html
#	docs/reference/correlation_data.html
#	docs/reference/correlation_plot.html
#	docs/reference/correlation_plots.html
#	docs/reference/cov_filter.html
#	docs/reference/create_phyloseq.html
#	docs/reference/create_pub_table.html
#	docs/reference/get_alpha_diversity_measures.html
#	docs/reference/get_color_palette.html
#	docs/reference/heat_tree_parameters.html
#	docs/reference/heat_tree_plots.html
#	docs/reference/index.html
#	docs/reference/is_analyzed_format.html
#	docs/reference/is_basic_format.html
#	docs/reference/is_phyloseq_format.html
#	docs/reference/is_raw_format.html
#	docs/reference/metacoder_comp_func_1.html
#	docs/reference/order_metacoder_data.html
#	docs/reference/ordination_plot.html
#	docs/reference/otu_id_filter.html
#	docs/reference/otu_prevalence_filter.html
#	docs/reference/otu_proportion_filter.html
#	docs/reference/output_dir.html
#	docs/reference/parse_taxonomy_silva_128.html
#	docs/reference/permanova.html
#	docs/reference/phyloseq_silva_2.html
#	docs/reference/phyloseq_silva_3.html
#	docs/reference/pick_new_outgroup.html
#	docs/reference/pipe.html
#	docs/reference/plot_limits.html
#	docs/reference/raw_silva_2.html
#	docs/reference/raw_silva_3.html
#	docs/reference/root_by_longest_edge.html
#	docs/reference/root_phyloseq_tree.html
#	docs/reference/sample_id_filter.html
#	docs/reference/save_correlation_plots.html
#	docs/reference/save_heat_tree_plots.html
#	docs/reference/save_ordination_plots.html
#	docs/reference/save_top_coefficients_barplot.html
#	docs/reference/scico_palette.html
#	docs/reference/stacked_barplot.html
#	docs/reference/taxa_prevalence_filter.html
#	docs/reference/taxon_id_filter.html
#	docs/reference/top_coefficients_barplot.html
#	docs/reference/transformer.html
#	docs/reference/transposer.html
#	docs/reference/treatment_matrix.html
#	docs/reference/validate_MicrobiomeR_format.html
#	docs/reference/viridis_magma_palette.html
#	docs/reference/viridis_palette.html
#	docs/reference/vlookup.html
#	docs/reference/which_format.html
#	man/heat_tree_plots.Rd
#	man/ordination_plot.Rd
#	man/save_barplot.Rd
#	man/stacked_barplot.Rd
grabear and others added 12 commits February 22, 2019 14:44
# Conflicts:
#	DESCRIPTION
#	NEWS.md
#	R/barplot.R
#	R/ordination.R
#	docs/CODE_OF_CONDUCT.html
#	docs/CONTRIBUTING.html
#	docs/ISSUE_TEMPLATE.html
#	docs/LICENSE-text.html
#	docs/PULL_REQUEST_TEMPLATE.html
#	docs/articles/about.html
#	docs/articles/analysis.html
#	docs/articles/analysis_files/figure-html/unnamed-chunk-10-1.png
#	docs/articles/analysis_files/figure-html/unnamed-chunk-11-1.png
#	docs/articles/analysis_files/figure-html/unnamed-chunk-12-1.png
#	docs/articles/analysis_files/figure-html/unnamed-chunk-13-1.png
#	docs/articles/analysis_files/figure-html/unnamed-chunk-13-2.png
#	docs/articles/analysis_files/figure-html/unnamed-chunk-13-3.png
#	docs/articles/analysis_files/figure-html/unnamed-chunk-13-4.png
#	docs/articles/color-palettes.html
#	docs/articles/color-palettes_files/figure-html/unnamed-chunk-1-1.png
#	docs/articles/color-palettes_files/figure-html/unnamed-chunk-2-1.png
#	docs/articles/color-palettes_files/figure-html/unnamed-chunk-2-2.png
#	docs/articles/color-palettes_files/figure-html/unnamed-chunk-3-1.png
#	docs/articles/color-palettes_files/figure-html/unnamed-chunk-4-1.png
#	docs/articles/color-palettes_files/figure-html/unnamed-chunk-5-1.png
#	docs/articles/data-wrangling.html
#	docs/articles/filtering.html
#	docs/articles/index.html
#	docs/articles/introduction.html
#	docs/authors.html
#	docs/index.html
#	docs/news/index.html
#	docs/reference/MicrobiomeR.html
#	docs/reference/MicrobiomeR_Formats.html
#	docs/reference/MicrobiomeR_Workflow.html
#	docs/reference/alpha_diversity_measures.html
#	docs/reference/alpha_diversity_plot.html
#	docs/reference/as_MicrobiomeR_format.html
#	docs/reference/as_analyzed_format.html
#	docs/reference/as_basic_format.html
#	docs/reference/as_custom_format.html
#	docs/reference/as_phyloseq_format.html
#	docs/reference/as_raw_format.html
#	docs/reference/combination_palette.html
#	docs/reference/correlation_data.html
#	docs/reference/correlation_plot.html
#	docs/reference/correlation_plots.html
#	docs/reference/cov_filter.html
#	docs/reference/create_phyloseq.html
#	docs/reference/create_pub_table.html
#	docs/reference/get_color_palette.html
#	docs/reference/heat_tree_parameters.html
#	docs/reference/heat_tree_plots.html
#	docs/reference/index.html
#	docs/reference/is_analyzed_format.html
#	docs/reference/is_basic_format.html
#	docs/reference/is_phyloseq_format.html
#	docs/reference/is_raw_format.html
#	docs/reference/metacoder_comp_func_1.html
#	docs/reference/order_metacoder_data.html
#	docs/reference/ordination_plot.html
#	docs/reference/otu_id_filter.html
#	docs/reference/otu_prevalence_filter.html
#	docs/reference/otu_proportion_filter.html
#	docs/reference/output_dir.html
#	docs/reference/parse_taxonomy_silva_128.html
#	docs/reference/permanova.html
#	docs/reference/phyloseq_silva_2.html
#	docs/reference/phyloseq_silva_3.html
#	docs/reference/pick_new_outgroup.html
#	docs/reference/pipe.html
#	docs/reference/plot_limits.html
#	docs/reference/raw_silva_2.html
#	docs/reference/raw_silva_3.html
#	docs/reference/root_by_longest_edge.html
#	docs/reference/root_phyloseq_tree.html
#	docs/reference/sample_id_filter.html
#	docs/reference/save_alpha_diversity_plots.html
#	docs/reference/save_correlation_plots.html
#	docs/reference/save_heat_tree_plots.html
#	docs/reference/save_ordination_plots.html
#	docs/reference/save_stacked_barplots.html
#	docs/reference/save_top_coefficients_barplot.html
#	docs/reference/scico_palette.html
#	docs/reference/stacked_barplot.html
#	docs/reference/taxa_prevalence_filter.html
#	docs/reference/taxon_id_filter.html
#	docs/reference/top_coefficients_barplot.html
#	docs/reference/transformer.html
#	docs/reference/transposer.html
#	docs/reference/treatment_matrix.html
#	docs/reference/validate_MicrobiomeR_format.html
#	docs/reference/viridis_magma_palette.html
#	docs/reference/viridis_palette.html
#	docs/reference/vlookup.html
#	docs/reference/which_format.html
@sdhutchins
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sdhutchins commented Feb 27, 2019

Add the codecov token to .travis.yml.

env:
  global:
    - _R_CHECK_FORCE_SUGGESTS_=false
    - R_REMOTES_NO_ERRORS_FROM_WARNINGS=true
    - CODECOV_TOKEN=2ff74b01-00e8-4e2f-9cc7-1f90ca17e480

@grabear
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grabear commented Feb 27, 2019

@sdhutchins If this build is successful it's going to take about 25 mins. And then I'm assuming another 30 mins to get it merged into master.

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Everything looks great! Yayyyyyyyyy

@sdhutchins sdhutchins merged commit 0743abc into dev-master Feb 27, 2019
@grabear grabear mentioned this pull request Feb 27, 2019
@sdhutchins sdhutchins deleted the joss-branch2 branch March 1, 2019 00:10
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