diff --git a/articles/manipulation.html b/articles/manipulation.html index e52f612..fede348 100644 --- a/articles/manipulation.html +++ b/articles/manipulation.html @@ -89,9 +89,9 @@

Yagmur yagmur.simsek@hsrw.org -

2024-08-21

+

2024-08-26

- Source: vignettes/articles/manipulation.Rmd + Source: vignettes/articles/manipulation.Rmd @@ -387,7 +387,7 @@

Session info## [19] sass_0.4.9 bslib_0.8.0 ## [21] htmlwidgets_1.6.4 desc_1.4.3 ## [23] sandwich_3.1-0 plyr_1.8.9 -## [25] DECIPHER_3.1.4 httr2_1.0.2 +## [25] DECIPHER_3.1.4 httr2_1.0.3 ## [27] plotly_4.10.4 zoo_1.8-12 ## [29] cachem_1.1.0 igraph_2.0.3 ## [31] lifecycle_1.0.4 pkgconfig_2.0.3 diff --git a/articles/miaTime.html b/articles/miaTime.html index 58ca0c3..c80b40a 100644 --- a/articles/miaTime.html +++ b/articles/miaTime.html @@ -89,9 +89,9 @@

Yagmur -

2024-08-21

+

2024-08-26

- Source: vignettes/miaTime.Rmd + Source: vignettes/miaTime.Rmd @@ -160,7 +160,7 @@

Session info## [21] bslib_0.8.0 htmlwidgets_1.6.4 ## [23] desc_1.4.3 sandwich_3.1-0 ## [25] plyr_1.8.9 DECIPHER_3.1.4 -## [27] httr2_1.0.2 zoo_1.8-12 +## [27] httr2_1.0.3 zoo_1.8-12 ## [29] cachem_1.1.0 igraph_2.0.3 ## [31] lifecycle_1.0.4 pkgconfig_2.0.3 ## [33] rsvd_1.0.5 Matrix_1.7-0 diff --git a/articles/minimalgut.html b/articles/minimalgut.html index 1e4a56d..2e1e074 100644 --- a/articles/minimalgut.html +++ b/articles/minimalgut.html @@ -86,9 +86,9 @@

Sudarshan

Leo Lahti

-

2024-08-21

+

2024-08-26

- Source: vignettes/articles/minimalgut.Rmd + Source: vignettes/articles/minimalgut.Rmd @@ -450,7 +450,7 @@

Session info## [1] splines_4.4.1 ggplotify_0.1.2 ## [3] tibble_3.2.1 polyclip_1.10-7 ## [5] rpart_4.1.23 DirichletMultinomial_1.47.0 -## [7] lifecycle_1.0.4 httr2_1.0.2 +## [7] lifecycle_1.0.4 httr2_1.0.3 ## [9] lattice_0.22-6 MASS_7.3-61 ## [11] SnowballC_0.7.1 backports_1.5.0 ## [13] magrittr_2.0.3 Hmisc_5.1-3 diff --git a/authors.html b/authors.html index 8a16e50..0abd4a2 100644 --- a/authors.html +++ b/authors.html @@ -77,7 +77,7 @@

Authors and Citation

Citation

- Source: inst/CITATION + Source: inst/CITATION
diff --git a/pkgdown.yml b/pkgdown.yml index 6148aea..54a814f 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: 2024-08-21T15:48Z +last_built: 2024-08-26T08:27Z diff --git a/reference/SilvermanAGutData.html b/reference/SilvermanAGutData.html index f366d6c..e6f456f 100644 --- a/reference/SilvermanAGutData.html +++ b/reference/SilvermanAGutData.html @@ -70,7 +70,7 @@

SilvermanAGutData

- Source: R/data.R + Source: R/data.R
diff --git a/reference/getBaselineDivergence.html b/reference/getBaselineDivergence.html index 1aa5f45..dbd247f 100644 --- a/reference/getBaselineDivergence.html +++ b/reference/getBaselineDivergence.html @@ -61,7 +61,7 @@

Beta diversity between the baseline and later time steps

- Source: R/getBaselineDivergence.R + Source: R/getBaselineDivergence.R
diff --git a/reference/getStepwiseDivergence.html b/reference/getStepwiseDivergence.html index ab166eb..bfc447e 100644 --- a/reference/getStepwiseDivergence.html +++ b/reference/getStepwiseDivergence.html @@ -60,7 +60,7 @@

Beta diversity between consecutive time steps

- Source: R/getStepwiseDivergence.R + Source: R/getStepwiseDivergence.R
diff --git a/reference/getTsMeasure.html b/reference/getTsMeasure.html new file mode 100644 index 0000000..64b50b1 --- /dev/null +++ b/reference/getTsMeasure.html @@ -0,0 +1,139 @@ + +Get Time Series Measures — getTsMeasure • miaTime + + +
+
+ + + +
+
+
+

Get Time Series Measures

+ Source: R/getTsMeasure.R + +
+ +
+

Calculate various time series measures (e.g., ACF, PACF) +from a specified column in the colData of a TreeSE object.

+
+ +
+ 
getTsMeasure(x, ...)
+
+# S4 method for class 'TreeSummarizedExperiment'
+getTsMeasure(x, time.field = "Time.hr", measures = c("acf", "pacf"), ...)
+
+ +
+

Arguments

+ + +
x
+

A +SummarizedExperiment +object.

+ + +
...
+

Additional arguments passed to specific time series functions.

+ + +
time.field
+

Character scalar. Specifies the name of the +time series field in colData. (Default: "Time.hr")

+ + +
measures
+

Character vector. Specifies the time series measures +to compute. Supported measures include "acf", "pacf","Box.test", and "arima". +(Default: "c("acf", "pacf")")

+ +
+
+

Value

+

A list containing the results of the requested time series measures.

+
+ +
+

Examples

+ 

+data(minimalgut)
+tse <- minimalgut
+result <- getTsMeasure(tse, time.field = "Time.hr", measure = "acf")
+
+
+
+
+ +
+ + +
+

Developed by Leo Lahti, Yagmur Simsek.

+
+ +
+

Site built with pkgdown 2.1.0.

+
+ +
+ + + + + + + + diff --git a/reference/hitchip1006.html b/reference/hitchip1006.html index fd99d41..64bf45b 100644 --- a/reference/hitchip1006.html +++ b/reference/hitchip1006.html @@ -59,7 +59,7 @@

HITChip Atlas with 1006 Western Adults

- Source: R/data.R + Source: R/data.R
diff --git a/reference/index.html b/reference/index.html index 01ab2be..b0bb763 100644 --- a/reference/index.html +++ b/reference/index.html @@ -75,6 +75,10 @@

All functions getStepwiseDivergence() getTimeDivergence()

Beta diversity between consecutive time steps

+ +

getTsMeasure()

+ +

Get Time Series Measures

hitchip1006

diff --git a/reference/minimalgut.html b/reference/minimalgut.html index 58b28e5..aa36974 100644 --- a/reference/minimalgut.html +++ b/reference/minimalgut.html @@ -61,7 +61,7 @@

Human Gut Minimal Microbiome Profiling Data

- Source: R/data.R + Source: R/data.R
diff --git a/reference/temporalMicrobiome20.html b/reference/temporalMicrobiome20.html index c0875e6..1170970 100644 --- a/reference/temporalMicrobiome20.html +++ b/reference/temporalMicrobiome20.html @@ -60,7 +60,7 @@

Gut Microbiome Profiling 20 Belgian Women

- Source: R/data.R + Source: R/data.R
diff --git a/sitemap.xml b/sitemap.xml index 2800f97..615e5ae 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -10,6 +10,7 @@ /reference/SilvermanAGutData.html /reference/getBaselineDivergence.html /reference/getStepwiseDivergence.html +/reference/getTsMeasure.html /reference/hitchip1006.html /reference/index.html /reference/minimalgut.html