-library(miaTime)
-#> Loading required package: ggplot2
-#> Loading required package: mia
-#> Loading required package: MultiAssayExperiment
-#> Loading required package: SummarizedExperiment
-#> Loading required package: MatrixGenerics
-#> Loading required package: matrixStats
-#>
-#> Attaching package: 'MatrixGenerics'
-#> The following objects are masked from 'package:matrixStats':
-#>
-#> colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
-#> colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
-#> colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
-#> colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
-#> colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
-#> colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
-#> colWeightedMeans, colWeightedMedians, colWeightedSds,
-#> colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
-#> rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
-#> rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
-#> rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
-#> rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
-#> rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
-#> rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
-#> rowWeightedSds, rowWeightedVars
-#> Loading required package: GenomicRanges
-#> Loading required package: stats4
-#> Loading required package: BiocGenerics
-#>
-#> Attaching package: 'BiocGenerics'
-#> The following objects are masked from 'package:stats':
-#>
-#> IQR, mad, sd, var, xtabs
-#> The following objects are masked from 'package:base':
-#>
-#> anyDuplicated, aperm, append, as.data.frame, basename, cbind,
-#> colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
-#> get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
-#> match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
-#> Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
-#> table, tapply, union, unique, unsplit, which.max, which.min
-#> Loading required package: S4Vectors
-#>
-#> Attaching package: 'S4Vectors'
-#> The following object is masked from 'package:utils':
-#>
-#> findMatches
-#> The following objects are masked from 'package:base':
-#>
-#> expand.grid, I, unname
-#> Loading required package: IRanges
-#> Loading required package: GenomeInfoDb
-#> Loading required package: Biobase
-#> Welcome to Bioconductor
-#>
-#> Vignettes contain introductory material; view with
-#> 'browseVignettes()'. To cite Bioconductor, see
-#> 'citation("Biobase")', and for packages 'citation("pkgname")'.
-#>
-#> Attaching package: 'Biobase'
-#> The following object is masked from 'package:MatrixGenerics':
-#>
-#> rowMedians
-#> The following objects are masked from 'package:matrixStats':
-#>
-#> anyMissing, rowMedians
-#> Loading required package: SingleCellExperiment
-#> Loading required package: TreeSummarizedExperiment
-#> Loading required package: Biostrings
-#> Loading required package: XVector
-#>
-#> Attaching package: 'Biostrings'
-#> The following object is masked from 'package:base':
-#>
-#> strsplit
-#> This is mia version 1.15.3
-#> - Online documentation and vignettes: https://microbiome.github.io/mia/
-#> - Online book 'Orchestrating Microbiome Analysis (OMA)': https://microbiome.github.io/OMA/docs/devel/
+library(miaTime)
Sorting samples
@@ -217,29 +139,6 @@ Storing time information wit
# Load packages
library(lubridate)
-#>
-#> Attaching package: 'lubridate'
-#> The following objects are masked from 'package:Biostrings':
-#>
-#> intersect, setdiff, union
-#> The following objects are masked from 'package:GenomicRanges':
-#>
-#> intersect, setdiff, union
-#> The following object is masked from 'package:GenomeInfoDb':
-#>
-#> intersect
-#> The following objects are masked from 'package:IRanges':
-#>
-#> %within%, intersect, setdiff, union
-#> The following objects are masked from 'package:S4Vectors':
-#>
-#> intersect, second, second<-, setdiff, union
-#> The following objects are masked from 'package:BiocGenerics':
-#>
-#> intersect, setdiff, union
-#> The following objects are masked from 'package:base':
-#>
-#> date, intersect, setdiff, union
# Time is given in days in the demo data.
# Convert days to seconds
@@ -363,44 +262,6 @@ Operations per unit
library(dplyr)
-#>
-#> Attaching package: 'dplyr'
-#> The following objects are masked from 'package:mia':
-#>
-#> full_join, inner_join, left_join, right_join
-#> The following objects are masked from 'package:Biostrings':
-#>
-#> collapse, intersect, setdiff, setequal, union
-#> The following object is masked from 'package:XVector':
-#>
-#> slice
-#> The following object is masked from 'package:Biobase':
-#>
-#> combine
-#> The following objects are masked from 'package:GenomicRanges':
-#>
-#> intersect, setdiff, union
-#> The following object is masked from 'package:GenomeInfoDb':
-#>
-#> intersect
-#> The following objects are masked from 'package:IRanges':
-#>
-#> collapse, desc, intersect, setdiff, slice, union
-#> The following objects are masked from 'package:S4Vectors':
-#>
-#> first, intersect, rename, setdiff, setequal, union
-#> The following objects are masked from 'package:BiocGenerics':
-#>
-#> combine, intersect, setdiff, union
-#> The following object is masked from 'package:matrixStats':
-#>
-#> count
-#> The following objects are masked from 'package:stats':
-#>
-#> filter, lag
-#> The following objects are masked from 'package:base':
-#>
-#> intersect, setdiff, setequal, union
colData(tse) <- colData(tse) |>
as.data.frame() |>
@@ -455,8 +316,7 @@ Session info#> [13] GenomeInfoDb_1.42.0 IRanges_2.40.0
#> [15] S4Vectors_0.44.0 BiocGenerics_0.52.0
#> [17] MatrixGenerics_1.18.0 matrixStats_1.4.1
-#> [19] ggplot2_3.5.1 knitr_1.48
-#> [21] BiocStyle_2.34.0
+#> [19] knitr_1.48 BiocStyle_2.34.0
#>
#> loaded via a namespace (and not attached):
#> [1] rstudioapi_0.17.1 jsonlite_1.8.9
@@ -483,38 +343,38 @@ Session info#> [43] beachmat_2.22.0 timechange_0.3.0
#> [45] fansi_1.0.6 mgcv_1.9-1
#> [47] httr_1.4.7 abind_1.4-8
-#> [49] compiler_4.4.1 withr_3.0.2
-#> [51] htmlTable_2.4.3 backports_1.5.0
-#> [53] BiocParallel_1.40.0 viridis_0.6.5
-#> [55] DBI_1.2.3 MASS_7.3-61
-#> [57] DelayedArray_0.32.0 bluster_1.16.0
-#> [59] permute_0.9-7 tools_4.4.1
-#> [61] vipor_0.4.7 foreign_0.8-87
-#> [63] beeswarm_0.4.0 ape_5.8
-#> [65] nnet_7.3-19 glue_1.8.0
-#> [67] nlme_3.1-166 grid_4.4.1
-#> [69] checkmate_2.3.2 cluster_2.1.6
-#> [71] reshape2_1.4.4 generics_0.1.3
-#> [73] lpSolve_5.6.21 gtable_0.3.6
-#> [75] mediation_4.5.0 tidyr_1.3.1
-#> [77] data.table_1.16.2 BiocSingular_1.22.0
-#> [79] ScaledMatrix_1.14.0 utf8_1.2.4
-#> [81] ggrepel_0.9.6 pillar_1.9.0
-#> [83] stringr_1.5.1 yulab.utils_0.1.7
-#> [85] splines_4.4.1 treeio_1.30.0
-#> [87] lattice_0.22-6 tidyselect_1.2.1
-#> [89] DirichletMultinomial_1.48.0 scuttle_1.16.0
-#> [91] gridExtra_2.3 bookdown_0.41
-#> [93] xfun_0.48 rbiom_1.0.3
-#> [95] stringi_1.8.4 UCSC.utils_1.2.0
-#> [97] lazyeval_0.2.2 yaml_2.3.10
-#> [99] boot_1.3-31 evaluate_1.0.1
-#> [101] codetools_0.2-20 tibble_3.2.1
-#> [103] BiocManager_1.30.25 cli_3.6.3
-#> [105] RcppParallel_5.1.9 rpart_4.1.23
-#> [107] systemfonts_1.1.0 munsell_0.5.1
-#> [109] jquerylib_0.1.4 Rcpp_1.0.13
-#> [111] parallel_4.4.1 pkgdown_2.1.1
+#> [49] compiler_4.4.1 htmlTable_2.4.3
+#> [51] backports_1.5.0 BiocParallel_1.40.0
+#> [53] viridis_0.6.5 DBI_1.2.3
+#> [55] MASS_7.3-61 DelayedArray_0.32.0
+#> [57] bluster_1.16.0 permute_0.9-7
+#> [59] tools_4.4.1 vipor_0.4.7
+#> [61] foreign_0.8-87 beeswarm_0.4.0
+#> [63] ape_5.8 nnet_7.3-19
+#> [65] glue_1.8.0 nlme_3.1-166
+#> [67] grid_4.4.1 checkmate_2.3.2
+#> [69] cluster_2.1.6 reshape2_1.4.4
+#> [71] lpSolve_5.6.21 generics_0.1.3
+#> [73] gtable_0.3.6 mediation_4.5.0
+#> [75] tidyr_1.3.1 data.table_1.16.2
+#> [77] BiocSingular_1.22.0 ScaledMatrix_1.14.0
+#> [79] utf8_1.2.4 ggrepel_0.9.6
+#> [81] pillar_1.9.0 stringr_1.5.1
+#> [83] yulab.utils_0.1.7 splines_4.4.1
+#> [85] treeio_1.30.0 lattice_0.22-6
+#> [87] tidyselect_1.2.1 DirichletMultinomial_1.48.0
+#> [89] scuttle_1.16.0 gridExtra_2.3
+#> [91] bookdown_0.41 xfun_0.48
+#> [93] rbiom_1.0.3 stringi_1.8.4
+#> [95] UCSC.utils_1.2.0 lazyeval_0.2.2
+#> [97] yaml_2.3.10 boot_1.3-31
+#> [99] evaluate_1.0.1 codetools_0.2-20
+#> [101] tibble_3.2.1 BiocManager_1.30.25
+#> [103] cli_3.6.3 RcppParallel_5.1.9
+#> [105] rpart_4.1.23 systemfonts_1.1.0
+#> [107] munsell_0.5.1 jquerylib_0.1.4
+#> [109] Rcpp_1.0.13 parallel_4.4.1
+#> [111] pkgdown_2.1.1 ggplot2_3.5.1
#> [113] sparseMatrixStats_1.18.0 lme4_1.1-35.5
#> [115] slam_0.1-54 mvtnorm_1.3-1
#> [117] decontam_1.26.0 viridisLite_0.4.2
diff --git a/articles/miaTime.html b/articles/miaTime.html
index fcd13dd..d9ba9a6 100644
--- a/articles/miaTime.html
+++ b/articles/miaTime.html
@@ -82,9 +82,9 @@
miaTime: Microbiome Time Series Analysis
- 2024-11-08
+ 2024-11-11
- Source: vignettes/miaTime.Rmd
+ Source: vignettes/miaTime.Rmd
miaTime.Rmd
@@ -113,7 +113,6 @@ Load the package
library(miaTime)
-#> Loading required package: ggplot2
#> Loading required package: mia
#> Loading required package: MultiAssayExperiment
#> Loading required package: SummarizedExperiment
@@ -276,6 +275,7 @@ Visualize time series
library(miaViz)
+#> Loading required package: ggplot2
#> Loading required package: ggraph
#>
#> Attaching package: 'miaViz'
@@ -319,15 +319,15 @@ Session info#>
#> other attached packages:
#> [1] miaViz_1.14.0 ggraph_2.2.1
-#> [3] miaTime_0.99.0 mia_1.15.3
-#> [5] TreeSummarizedExperiment_2.14.0 Biostrings_2.74.0
-#> [7] XVector_0.46.0 SingleCellExperiment_1.28.0
-#> [9] MultiAssayExperiment_1.32.0 SummarizedExperiment_1.36.0
-#> [11] Biobase_2.66.0 GenomicRanges_1.58.0
-#> [13] GenomeInfoDb_1.42.0 IRanges_2.40.0
-#> [15] S4Vectors_0.44.0 BiocGenerics_0.52.0
-#> [17] MatrixGenerics_1.18.0 matrixStats_1.4.1
-#> [19] ggplot2_3.5.1 knitr_1.48
+#> [3] ggplot2_3.5.1 miaTime_0.99.0
+#> [5] mia_1.15.3 TreeSummarizedExperiment_2.14.0
+#> [7] Biostrings_2.74.0 XVector_0.46.0
+#> [9] SingleCellExperiment_1.28.0 MultiAssayExperiment_1.32.0
+#> [11] SummarizedExperiment_1.36.0 Biobase_2.66.0
+#> [13] GenomicRanges_1.58.0 GenomeInfoDb_1.42.0
+#> [15] IRanges_2.40.0 S4Vectors_0.44.0
+#> [17] BiocGenerics_0.52.0 MatrixGenerics_1.18.0
+#> [19] matrixStats_1.4.1 knitr_1.48
#> [21] BiocStyle_2.34.0
#>
#> loaded via a namespace (and not attached):
diff --git a/articles/minimalgut.html b/articles/minimalgut.html
index 8e40083..fa3ed9e 100644
--- a/articles/minimalgut.html
+++ b/articles/minimalgut.html
@@ -82,9 +82,9 @@
Minimal gut bioreactor examples
- 2024-11-08
+ 2024-11-11
- Source: vignettes/articles/minimalgut.Rmd
+ Source: vignettes/articles/minimalgut.Rmd
minimalgut.Rmd
@@ -100,84 +100,6 @@ Minimal gut microbiomecolData
.
library(miaTime)
-#> Loading required package: ggplot2
-#> Loading required package: mia
-#> Loading required package: MultiAssayExperiment
-#> Loading required package: SummarizedExperiment
-#> Loading required package: MatrixGenerics
-#> Loading required package: matrixStats
-#>
-#> Attaching package: 'MatrixGenerics'
-#> The following objects are masked from 'package:matrixStats':
-#>
-#> colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
-#> colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
-#> colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
-#> colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
-#> colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
-#> colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
-#> colWeightedMeans, colWeightedMedians, colWeightedSds,
-#> colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
-#> rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
-#> rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
-#> rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
-#> rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
-#> rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
-#> rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
-#> rowWeightedSds, rowWeightedVars
-#> Loading required package: GenomicRanges
-#> Loading required package: stats4
-#> Loading required package: BiocGenerics
-#>
-#> Attaching package: 'BiocGenerics'
-#> The following objects are masked from 'package:stats':
-#>
-#> IQR, mad, sd, var, xtabs
-#> The following objects are masked from 'package:base':
-#>
-#> anyDuplicated, aperm, append, as.data.frame, basename, cbind,
-#> colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
-#> get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
-#> match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
-#> Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
-#> table, tapply, union, unique, unsplit, which.max, which.min
-#> Loading required package: S4Vectors
-#>
-#> Attaching package: 'S4Vectors'
-#> The following object is masked from 'package:utils':
-#>
-#> findMatches
-#> The following objects are masked from 'package:base':
-#>
-#> expand.grid, I, unname
-#> Loading required package: IRanges
-#> Loading required package: GenomeInfoDb
-#> Loading required package: Biobase
-#> Welcome to Bioconductor
-#>
-#> Vignettes contain introductory material; view with
-#> 'browseVignettes()'. To cite Bioconductor, see
-#> 'citation("Biobase")', and for packages 'citation("pkgname")'.
-#>
-#> Attaching package: 'Biobase'
-#> The following object is masked from 'package:MatrixGenerics':
-#>
-#> rowMedians
-#> The following objects are masked from 'package:matrixStats':
-#>
-#> anyMissing, rowMedians
-#> Loading required package: SingleCellExperiment
-#> Loading required package: TreeSummarizedExperiment
-#> Loading required package: Biostrings
-#> Loading required package: XVector
-#>
-#> Attaching package: 'Biostrings'
-#> The following object is masked from 'package:base':
-#>
-#> strsplit
-#> This is mia version 1.15.3
-#> - Online documentation and vignettes: https://microbiome.github.io/mia/
-#> - Online book 'Orchestrating Microbiome Analysis (OMA)': https://microbiome.github.io/OMA/docs/devel/
data(minimalgut)
tse <- minimalgut
@@ -220,7 +142,6 @@ Community dynamics
library(scater)
-#> Loading required package: scuttle
# Create a time series plot for divergence
p <- plotColData(
@@ -237,12 +158,6 @@ Visualizing selected taxamiaViz::plotSeries()
function.
library(miaViz)
-#> Loading required package: ggraph
-#>
-#> Attaching package: 'miaViz'
-#> The following object is masked from 'package:mia':
-#>
-#> plotNMDS
# Plot certain feature by time
p <- plotSeries(
@@ -288,11 +203,7 @@ Visualize the rate (slope) of di
) +
# Add line between points
geom_line(aes(group = .data[["colour_by"]], colour = .data[["colour_by"]]))
-p
-#> Warning: Removed 3 rows containing missing values or values outside the scale range
-#> (`geom_point()`).
-#> Warning: Removed 3 rows containing missing values or values outside the scale range
-#> (`geom_line()`).
+p
@@ -302,44 +213,6 @@ Moving average of the slope
library(dplyr)
-#>
-#> Attaching package: 'dplyr'
-#> The following objects are masked from 'package:mia':
-#>
-#> full_join, inner_join, left_join, right_join
-#> The following objects are masked from 'package:Biostrings':
-#>
-#> collapse, intersect, setdiff, setequal, union
-#> The following object is masked from 'package:XVector':
-#>
-#> slice
-#> The following object is masked from 'package:Biobase':
-#>
-#> combine
-#> The following objects are masked from 'package:GenomicRanges':
-#>
-#> intersect, setdiff, union
-#> The following object is masked from 'package:GenomeInfoDb':
-#>
-#> intersect
-#> The following objects are masked from 'package:IRanges':
-#>
-#> collapse, desc, intersect, setdiff, slice, union
-#> The following objects are masked from 'package:S4Vectors':
-#>
-#> first, intersect, rename, setdiff, setequal, union
-#> The following objects are masked from 'package:BiocGenerics':
-#>
-#> combine, intersect, setdiff, union
-#> The following object is masked from 'package:matrixStats':
-#>
-#> count
-#> The following objects are masked from 'package:stats':
-#>
-#> filter, lag
-#> The following objects are masked from 'package:base':
-#>
-#> intersect, setdiff, setequal, union
# Calculate moving average with time window of 3 time points
tse[["sliding_divergence"]] <- colData(tse) |>
@@ -371,11 +244,7 @@ Moving average of the slope) +
# Add line between points
geom_line(aes(group = .data[["colour_by"]], colour = .data[["colour_by"]]))
-p
-#> Warning: Removed 9 rows containing missing values or values outside the scale range
-#> (`geom_point()`).
-#> Warning: Removed 3 rows containing missing values or values outside the scale range
-#> (`geom_line()`).
+p
# Load packages
library(lubridate)
-#>
-#> Attaching package: 'lubridate'
-#> The following objects are masked from 'package:Biostrings':
-#>
-#> intersect, setdiff, union
-#> The following objects are masked from 'package:GenomicRanges':
-#>
-#> intersect, setdiff, union
-#> The following object is masked from 'package:GenomeInfoDb':
-#>
-#> intersect
-#> The following objects are masked from 'package:IRanges':
-#>
-#> %within%, intersect, setdiff, union
-#> The following objects are masked from 'package:S4Vectors':
-#>
-#> intersect, second, second<-, setdiff, union
-#> The following objects are masked from 'package:BiocGenerics':
-#>
-#> intersect, setdiff, union
-#> The following objects are masked from 'package:base':
-#>
-#> date, intersect, setdiff, union
# Time is given in days in the demo data.
# Convert days to seconds
@@ -363,44 +262,6 @@ Operations per unit
library(dplyr)
-#>
-#> Attaching package: 'dplyr'
-#> The following objects are masked from 'package:mia':
-#>
-#> full_join, inner_join, left_join, right_join
-#> The following objects are masked from 'package:Biostrings':
-#>
-#> collapse, intersect, setdiff, setequal, union
-#> The following object is masked from 'package:XVector':
-#>
-#> slice
-#> The following object is masked from 'package:Biobase':
-#>
-#> combine
-#> The following objects are masked from 'package:GenomicRanges':
-#>
-#> intersect, setdiff, union
-#> The following object is masked from 'package:GenomeInfoDb':
-#>
-#> intersect
-#> The following objects are masked from 'package:IRanges':
-#>
-#> collapse, desc, intersect, setdiff, slice, union
-#> The following objects are masked from 'package:S4Vectors':
-#>
-#> first, intersect, rename, setdiff, setequal, union
-#> The following objects are masked from 'package:BiocGenerics':
-#>
-#> combine, intersect, setdiff, union
-#> The following object is masked from 'package:matrixStats':
-#>
-#> count
-#> The following objects are masked from 'package:stats':
-#>
-#> filter, lag
-#> The following objects are masked from 'package:base':
-#>
-#> intersect, setdiff, setequal, union
colData(tse) <- colData(tse) |>
as.data.frame() |>
@@ -455,8 +316,7 @@ Session info#> [13] GenomeInfoDb_1.42.0 IRanges_2.40.0
#> [15] S4Vectors_0.44.0 BiocGenerics_0.52.0
#> [17] MatrixGenerics_1.18.0 matrixStats_1.4.1
-#> [19] ggplot2_3.5.1 knitr_1.48
-#> [21] BiocStyle_2.34.0
+#> [19] knitr_1.48 BiocStyle_2.34.0
#>
#> loaded via a namespace (and not attached):
#> [1] rstudioapi_0.17.1 jsonlite_1.8.9
@@ -483,38 +343,38 @@ Session info#> [43] beachmat_2.22.0 timechange_0.3.0
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-#> [89] DirichletMultinomial_1.48.0 scuttle_1.16.0
-#> [91] gridExtra_2.3 bookdown_0.41
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-#> [95] stringi_1.8.4 UCSC.utils_1.2.0
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-#> [109] jquerylib_0.1.4 Rcpp_1.0.13
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+#> [53] viridis_0.6.5 DBI_1.2.3
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+#> [69] cluster_2.1.6 reshape2_1.4.4
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+#> [93] rbiom_1.0.3 stringi_1.8.4
+#> [95] UCSC.utils_1.2.0 lazyeval_0.2.2
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+#> [99] evaluate_1.0.1 codetools_0.2-20
+#> [101] tibble_3.2.1 BiocManager_1.30.25
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+#> [105] rpart_4.1.23 systemfonts_1.1.0
+#> [107] munsell_0.5.1 jquerylib_0.1.4
+#> [109] Rcpp_1.0.13 parallel_4.4.1
+#> [111] pkgdown_2.1.1 ggplot2_3.5.1
#> [113] sparseMatrixStats_1.18.0 lme4_1.1-35.5
#> [115] slam_0.1-54 mvtnorm_1.3-1
#> [117] decontam_1.26.0 viridisLite_0.4.2
diff --git a/articles/miaTime.html b/articles/miaTime.html
index fcd13dd..d9ba9a6 100644
--- a/articles/miaTime.html
+++ b/articles/miaTime.html
@@ -82,9 +82,9 @@
miaTime: Microbiome Time Series Analysis
- 2024-11-08
+ 2024-11-11
- Source: vignettes/miaTime.Rmd
+ Source: vignettes/miaTime.Rmd
miaTime.Rmd
@@ -113,7 +113,6 @@ Load the package
library(miaTime)
-#> Loading required package: ggplot2
#> Loading required package: mia
#> Loading required package: MultiAssayExperiment
#> Loading required package: SummarizedExperiment
@@ -276,6 +275,7 @@ Visualize time series
library(miaViz)
+#> Loading required package: ggplot2
#> Loading required package: ggraph
#>
#> Attaching package: 'miaViz'
@@ -319,15 +319,15 @@ Session info#>
#> other attached packages:
#> [1] miaViz_1.14.0 ggraph_2.2.1
-#> [3] miaTime_0.99.0 mia_1.15.3
-#> [5] TreeSummarizedExperiment_2.14.0 Biostrings_2.74.0
-#> [7] XVector_0.46.0 SingleCellExperiment_1.28.0
-#> [9] MultiAssayExperiment_1.32.0 SummarizedExperiment_1.36.0
-#> [11] Biobase_2.66.0 GenomicRanges_1.58.0
-#> [13] GenomeInfoDb_1.42.0 IRanges_2.40.0
-#> [15] S4Vectors_0.44.0 BiocGenerics_0.52.0
-#> [17] MatrixGenerics_1.18.0 matrixStats_1.4.1
-#> [19] ggplot2_3.5.1 knitr_1.48
+#> [3] ggplot2_3.5.1 miaTime_0.99.0
+#> [5] mia_1.15.3 TreeSummarizedExperiment_2.14.0
+#> [7] Biostrings_2.74.0 XVector_0.46.0
+#> [9] SingleCellExperiment_1.28.0 MultiAssayExperiment_1.32.0
+#> [11] SummarizedExperiment_1.36.0 Biobase_2.66.0
+#> [13] GenomicRanges_1.58.0 GenomeInfoDb_1.42.0
+#> [15] IRanges_2.40.0 S4Vectors_0.44.0
+#> [17] BiocGenerics_0.52.0 MatrixGenerics_1.18.0
+#> [19] matrixStats_1.4.1 knitr_1.48
#> [21] BiocStyle_2.34.0
#>
#> loaded via a namespace (and not attached):
diff --git a/articles/minimalgut.html b/articles/minimalgut.html
index 8e40083..fa3ed9e 100644
--- a/articles/minimalgut.html
+++ b/articles/minimalgut.html
@@ -82,9 +82,9 @@
Minimal gut bioreactor examples
- 2024-11-08
+ 2024-11-11
- Source: vignettes/articles/minimalgut.Rmd
+ Source: vignettes/articles/minimalgut.Rmd
minimalgut.Rmd
@@ -100,84 +100,6 @@ Minimal gut microbiomecolData
.
library(miaTime)
-#> Loading required package: ggplot2
-#> Loading required package: mia
-#> Loading required package: MultiAssayExperiment
-#> Loading required package: SummarizedExperiment
-#> Loading required package: MatrixGenerics
-#> Loading required package: matrixStats
-#>
-#> Attaching package: 'MatrixGenerics'
-#> The following objects are masked from 'package:matrixStats':
-#>
-#> colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
-#> colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
-#> colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
-#> colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
-#> colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
-#> colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
-#> colWeightedMeans, colWeightedMedians, colWeightedSds,
-#> colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
-#> rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
-#> rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
-#> rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
-#> rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
-#> rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
-#> rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
-#> rowWeightedSds, rowWeightedVars
-#> Loading required package: GenomicRanges
-#> Loading required package: stats4
-#> Loading required package: BiocGenerics
-#>
-#> Attaching package: 'BiocGenerics'
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-#>
-#> IQR, mad, sd, var, xtabs
-#> The following objects are masked from 'package:base':
-#>
-#> anyDuplicated, aperm, append, as.data.frame, basename, cbind,
-#> colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
-#> get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
-#> match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
-#> Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,
-#> table, tapply, union, unique, unsplit, which.max, which.min
-#> Loading required package: S4Vectors
-#>
-#> Attaching package: 'S4Vectors'
-#> The following object is masked from 'package:utils':
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-#> findMatches
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-#> expand.grid, I, unname
-#> Loading required package: IRanges
-#> Loading required package: GenomeInfoDb
-#> Loading required package: Biobase
-#> Welcome to Bioconductor
-#>
-#> Vignettes contain introductory material; view with
-#> 'browseVignettes()'. To cite Bioconductor, see
-#> 'citation("Biobase")', and for packages 'citation("pkgname")'.
-#>
-#> Attaching package: 'Biobase'
-#> The following object is masked from 'package:MatrixGenerics':
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-#> rowMedians
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-#> anyMissing, rowMedians
-#> Loading required package: SingleCellExperiment
-#> Loading required package: TreeSummarizedExperiment
-#> Loading required package: Biostrings
-#> Loading required package: XVector
-#>
-#> Attaching package: 'Biostrings'
-#> The following object is masked from 'package:base':
-#>
-#> strsplit
-#> This is mia version 1.15.3
-#> - Online documentation and vignettes: https://microbiome.github.io/mia/
-#> - Online book 'Orchestrating Microbiome Analysis (OMA)': https://microbiome.github.io/OMA/docs/devel/
data(minimalgut)
tse <- minimalgut
@@ -220,7 +142,6 @@ Community dynamics
library(scater)
-#> Loading required package: scuttle
# Create a time series plot for divergence
p <- plotColData(
@@ -237,12 +158,6 @@ Visualizing selected taxamiaViz::plotSeries()
function.
library(miaViz)
-#> Loading required package: ggraph
-#>
-#> Attaching package: 'miaViz'
-#> The following object is masked from 'package:mia':
-#>
-#> plotNMDS
# Plot certain feature by time
p <- plotSeries(
@@ -288,11 +203,7 @@ Visualize the rate (slope) of di
) +
# Add line between points
geom_line(aes(group = .data[["colour_by"]], colour = .data[["colour_by"]]))
-p
-#> Warning: Removed 3 rows containing missing values or values outside the scale range
-#> (`geom_point()`).
-#> Warning: Removed 3 rows containing missing values or values outside the scale range
-#> (`geom_line()`).
+p
@@ -302,44 +213,6 @@ Moving average of the slope
library(dplyr)
-#>
-#> Attaching package: 'dplyr'
-#> The following objects are masked from 'package:mia':
-#>
-#> full_join, inner_join, left_join, right_join
-#> The following objects are masked from 'package:Biostrings':
-#>
-#> collapse, intersect, setdiff, setequal, union
-#> The following object is masked from 'package:XVector':
-#>
-#> slice
-#> The following object is masked from 'package:Biobase':
-#>
-#> combine
-#> The following objects are masked from 'package:GenomicRanges':
-#>
-#> intersect, setdiff, union
-#> The following object is masked from 'package:GenomeInfoDb':
-#>
-#> intersect
-#> The following objects are masked from 'package:IRanges':
-#>
-#> collapse, desc, intersect, setdiff, slice, union
-#> The following objects are masked from 'package:S4Vectors':
-#>
-#> first, intersect, rename, setdiff, setequal, union
-#> The following objects are masked from 'package:BiocGenerics':
-#>
-#> combine, intersect, setdiff, union
-#> The following object is masked from 'package:matrixStats':
-#>
-#> count
-#> The following objects are masked from 'package:stats':
-#>
-#> filter, lag
-#> The following objects are masked from 'package:base':
-#>
-#> intersect, setdiff, setequal, union
# Calculate moving average with time window of 3 time points
tse[["sliding_divergence"]] <- colData(tse) |>
@@ -371,11 +244,7 @@ Moving average of the slope) +
# Add line between points
geom_line(aes(group = .data[["colour_by"]], colour = .data[["colour_by"]]))
-p
-#> Warning: Removed 9 rows containing missing values or values outside the scale range
-#> (`geom_point()`).
-#> Warning: Removed 3 rows containing missing values or values outside the scale range
-#> (`geom_line()`).
+p
Session info#> other attached packages:
#> [1] dplyr_1.1.4 miaViz_1.14.0
#> [3] ggraph_2.2.1 scater_1.34.0
-#> [5] scuttle_1.16.0 miaTime_0.99.0
-#> [7] mia_1.15.3 TreeSummarizedExperiment_2.14.0
-#> [9] Biostrings_2.74.0 XVector_0.46.0
-#> [11] SingleCellExperiment_1.28.0 MultiAssayExperiment_1.32.0
-#> [13] SummarizedExperiment_1.36.0 Biobase_2.66.0
-#> [15] GenomicRanges_1.58.0 GenomeInfoDb_1.42.0
-#> [17] IRanges_2.40.0 S4Vectors_0.44.0
-#> [19] BiocGenerics_0.52.0 MatrixGenerics_1.18.0
-#> [21] matrixStats_1.4.1 ggplot2_3.5.1
+#> [5] scuttle_1.16.0 ggplot2_3.5.1
+#> [7] miaTime_0.99.0 mia_1.15.3
+#> [9] TreeSummarizedExperiment_2.14.0 Biostrings_2.74.0
+#> [11] XVector_0.46.0 SingleCellExperiment_1.28.0
+#> [13] MultiAssayExperiment_1.32.0 SummarizedExperiment_1.36.0
+#> [15] Biobase_2.66.0 GenomicRanges_1.58.0
+#> [17] GenomeInfoDb_1.42.0 IRanges_2.40.0
+#> [19] S4Vectors_0.44.0 BiocGenerics_0.52.0
+#> [21] MatrixGenerics_1.18.0 matrixStats_1.4.1
#> [23] knitr_1.48 BiocStyle_2.34.0
#>
#> loaded via a namespace (and not attached):
@@ -457,8 +326,8 @@ Session info#> [65] BiocManager_1.30.25 fastmap_1.2.0
#> [67] boot_1.3-31 bluster_1.16.0
#> [69] fansi_1.0.6 digest_0.6.37
-#> [71] rsvd_1.0.5 R6_2.5.1
-#> [73] gridGraphics_0.5-1 textshaping_0.4.0
+#> [71] rsvd_1.0.5 gridGraphics_0.5-1
+#> [73] R6_2.5.1 textshaping_0.4.0
#> [75] colorspace_2.1-1 lpSolve_5.6.21
#> [77] utf8_1.2.4 tidyr_1.3.1
#> [79] generics_0.1.3 data.table_1.16.2
diff --git a/authors.html b/authors.html
index 1c24417..002856b 100644
--- a/authors.html
+++ b/authors.html
@@ -89,7 +89,7 @@ Authors and Citation
diff --git a/pkgdown.yml b/pkgdown.yml
index e30d42d..3eb19ce 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -5,4 +5,4 @@ articles:
articles/manipulation: manipulation.html
miaTime: miaTime.html
articles/minimalgut: minimalgut.html
-last_built: 2024-11-08T12:04Z
+last_built: 2024-11-11T09:04Z
diff --git a/reference/SilvermanAGutData.html b/reference/SilvermanAGutData.html
index 5ecbb9c..b306a8a 100644
--- a/reference/SilvermanAGutData.html
+++ b/reference/SilvermanAGutData.html
@@ -70,7 +70,7 @@
diff --git a/reference/addBaselineDivergence.html b/reference/addBaselineDivergence.html
index 44d56b0..d4dd117 100644
--- a/reference/addBaselineDivergence.html
+++ b/reference/addBaselineDivergence.html
@@ -59,7 +59,7 @@
Beta diversity between the baseline and later time steps
- Source: R/AllGenerics.R, R/getBaselineDivergence.R
+ Source: R/AllGenerics.R, R/getBaselineDivergence.R
addBaselineDivergence.Rd
diff --git a/reference/addStepwiseDivergence.html b/reference/addStepwiseDivergence.html
index a2d0d03..f73affc 100644
--- a/reference/addStepwiseDivergence.html
+++ b/reference/addStepwiseDivergence.html
@@ -58,7 +58,7 @@
Beta diversity between consecutive time steps
- Source: R/AllGenerics.R, R/getStepwiseDivergence.R
+ Source: R/AllGenerics.R, R/getStepwiseDivergence.R
addStepwiseDivergence.Rd
diff --git a/reference/hitchip1006.html b/reference/hitchip1006.html
index 8789570..6df01ff 100644
--- a/reference/hitchip1006.html
+++ b/reference/hitchip1006.html
@@ -59,7 +59,7 @@
diff --git a/reference/index.html b/reference/index.html
index b6f4222..683899c 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -75,10 +75,6 @@ All functions getStepwiseDivergence() addStepwiseDivergence()
Beta diversity between consecutive time steps
-
-
- Short term Changes in Abundance
diff --git a/reference/miaTime-package.html b/reference/miaTime-package.html
index 2ee4c74..2a3dfc3 100644
--- a/reference/miaTime-package.html
+++ b/reference/miaTime-package.html
@@ -57,7 +57,7 @@
@@ -72,11 +72,11 @@ See also
diff --git a/reference/minimalgut.html b/reference/minimalgut.html
index 3b74ed3..fc4634a 100644
--- a/reference/minimalgut.html
+++ b/reference/minimalgut.html
@@ -61,7 +61,7 @@
Human Gut Minimal Microbiome Profiling Data
- Source: R/miaTime.R
+ Source: R/miaTime.R
minimalgut.Rd
diff --git a/reference/temporalMicrobiome20.html b/reference/temporalMicrobiome20.html
index 2acff92..404938d 100644
--- a/reference/temporalMicrobiome20.html
+++ b/reference/temporalMicrobiome20.html
@@ -60,7 +60,7 @@
Gut Microbiome Profiling 20 Belgian Women
- Source: R/miaTime.R
+ Source: R/miaTime.R
temporalMicrobiome20.Rd
diff --git a/sitemap.xml b/sitemap.xml
index 8ca0514..3ca194c 100644
--- a/sitemap.xml
+++ b/sitemap.xml
@@ -10,7 +10,6 @@
/reference/SilvermanAGutData.html /reference/addBaselineDivergence.html /reference/addStepwiseDivergence.html /reference/getShortTermChange.html /reference/hitchip1006.html /reference/index.html /reference/miaTime-package.html
Authors and Citation
diff --git a/reference/addBaselineDivergence.html b/reference/addBaselineDivergence.html
index 44d56b0..d4dd117 100644
--- a/reference/addBaselineDivergence.html
+++ b/reference/addBaselineDivergence.html
@@ -59,7 +59,7 @@
diff --git a/reference/addStepwiseDivergence.html b/reference/addStepwiseDivergence.html
index a2d0d03..f73affc 100644
--- a/reference/addStepwiseDivergence.html
+++ b/reference/addStepwiseDivergence.html
@@ -58,7 +58,7 @@
diff --git a/reference/hitchip1006.html b/reference/hitchip1006.html
index 8789570..6df01ff 100644
--- a/reference/hitchip1006.html
+++ b/reference/hitchip1006.html
@@ -59,7 +59,7 @@
Beta diversity between the baseline and later time steps
- Source:R/AllGenerics.R, R/getBaselineDivergence.R
+ Source: R/AllGenerics.R, R/getBaselineDivergence.R
addBaselineDivergence.RdBeta diversity between consecutive time steps
- Source:R/AllGenerics.R, R/getStepwiseDivergence.R
+ Source: R/AllGenerics.R, R/getStepwiseDivergence.R
addStepwiseDivergence.Rd
diff --git a/reference/index.html b/reference/index.html
index b6f4222..683899c 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -75,10 +75,6 @@ All functions
All functions getStepwiseDivergence() addStepwiseDivergence()
Beta diversity between consecutive time steps
-
-
- Short term Changes in Abundance
diff --git a/reference/miaTime-package.html b/reference/miaTime-package.html
index 2ee4c74..2a3dfc3 100644
--- a/reference/miaTime-package.html
+++ b/reference/miaTime-package.html
@@ -57,7 +57,7 @@
@@ -72,11 +72,11 @@ See also
diff --git a/reference/minimalgut.html b/reference/minimalgut.html
index 3b74ed3..fc4634a 100644
--- a/reference/minimalgut.html
+++ b/reference/minimalgut.html
@@ -61,7 +61,7 @@
Human Gut Minimal Microbiome Profiling Data
- Source: R/miaTime.R
+ Source: R/miaTime.R
minimalgut.Rd
diff --git a/reference/temporalMicrobiome20.html b/reference/temporalMicrobiome20.html
index 2acff92..404938d 100644
--- a/reference/temporalMicrobiome20.html
+++ b/reference/temporalMicrobiome20.html
@@ -60,7 +60,7 @@
Gut Microbiome Profiling 20 Belgian Women
- Source: R/miaTime.R
+ Source: R/miaTime.R
temporalMicrobiome20.Rd
diff --git a/sitemap.xml b/sitemap.xml
index 8ca0514..3ca194c 100644
--- a/sitemap.xml
+++ b/sitemap.xml
@@ -10,7 +10,6 @@
/reference/SilvermanAGutData.html /reference/addBaselineDivergence.html /reference/addStepwiseDivergence.html /reference/getShortTermChange.html /reference/hitchip1006.html /reference/index.html /reference/miaTime-package.html
Beta diversity between consecutive time steps
Short term Changes in Abundance
@@ -72,11 +72,11 @@
diff --git a/reference/minimalgut.html b/reference/minimalgut.html
index 3b74ed3..fc4634a 100644
--- a/reference/minimalgut.html
+++ b/reference/minimalgut.html
@@ -61,7 +61,7 @@
See also
Human Gut Minimal Microbiome Profiling Data
- Source:R/miaTime.R
+ Source: R/miaTime.R
minimalgut.RdGut Microbiome Profiling 20 Belgian Women
- Source:R/miaTime.R
+ Source: R/miaTime.R
temporalMicrobiome20.Rd