A Wokaty authored on 15/04/2025 15:54:06
A Wokaty authored on 15/04/2025 15:54:06
Gavin Rhys Lloyd authored on 19/02/2025 11:09:45
ANOVA interaction term now included in outputs
Gavin Rhys Lloyd authored on 28/01/2025 09:25:47
J Wokaty authored on 29/10/2024 14:43:04
J Wokaty authored on 29/10/2024 14:43:03
updated fold change to account for control_group param added to ttest
Gavin Rhys Lloyd authored on 01/07/2024 11:07:17
Gavin Rhys Lloyd authored on 27/06/2024 14:00:18
Gavin Rhys Lloyd authored on 27/06/2024 13:58:27
Gavin Rhys Lloyd authored on 27/06/2024 13:06:21
J Wokaty authored on 30/04/2024 15:20:29
J Wokaty authored on 30/04/2024 15:20:29
Gavin Rhys Lloyd authored on 31/01/2024 10:47:23
Gavin Rhys Lloyd authored on 31/01/2024 09:51:23
Gavin Rhys Lloyd authored on 31/01/2024 09:50:48
- get_description moved to struct and updated
Gavin Rhys Lloyd authored on 31/01/2024 09:48:31
J Wokaty authored on 24/10/2023 15:19:09
J Wokaty authored on 24/10/2023 15:19:09
Gavin Rhys Lloyd authored on 13/10/2023 20:00:43
| ... | ... |
@@ -147,5 +147,5 @@ Suggests: agricolae, |
| 147 | 147 |
rappdirs |
| 148 | 148 |
VignetteBuilder: knitr |
| 149 | 149 |
biocViews: WorkflowStep, Metabolomics |
| 150 |
-URL: https://github.com/computational-metabolomics/structToolbox |
|
| 150 |
+URL: https://github.com/computational-metabolomics/structToolbox, https://computational-metabolomics.github.io/structToolbox/ |
|
| 151 | 151 |
Roxygen: list(markdown = TRUE) |
- simplify computation of flags when applying fc threshold for consistency across methods
- better handling of NA when computing intervals for median and mean methods
Gavin Rhys Lloyd authored on 05/10/2023 10:25:32
Gavin Rhys Lloyd authored on 05/09/2023 15:08:44
Gavin Rhys Lloyd authored on 20/07/2023 10:54:48
Gavin Rhys Lloyd authored on 10/07/2023 13:00:50
Gavin Rhys Lloyd authored on 06/07/2023 19:55:35
due to roxygen no longer needing % to be escaped.
- add markdown flag to description file
- use text format for citations (includes markdown)
- remove % from descriptions (doesnt work with current implementation)
Gavin Rhys Lloyd authored on 06/07/2023 15:19:12
Gavin Rhys Lloyd authored on 06/07/2023 13:16:43
J Wokaty authored on 25/04/2023 15:15:09
J Wokaty authored on 25/04/2023 15:15:08
Gavin Rhys Lloyd authored on 06/02/2023 13:26:40
Gavin Rhys Lloyd authored on 23/01/2023 10:57:52
| ... | ... |
@@ -91,6 +91,8 @@ Collate: |
| 91 | 91 |
'mv_feature_filter_class.R' |
| 92 | 92 |
'mv_sample_filter_class.R' |
| 93 | 93 |
'nroot_transform_class.R' |
| 94 |
+ 'oplsr_class.R' |
|
| 95 |
+ 'oplsda_class.R' |
|
| 94 | 96 |
'pairs_filter_class.R' |
| 95 | 97 |
'paretoscale_class.R' |
| 96 | 98 |
'permutation_test_class.R' |
| ... | ... |
@@ -121,7 +123,7 @@ Imports: ggplot2, |
| 121 | 123 |
sp, |
| 122 | 124 |
stats, |
| 123 | 125 |
utils |
| 124 |
-RoxygenNote: 7.1.2 |
|
| 126 |
+RoxygenNote: 7.2.2 |
|
| 125 | 127 |
Suggests: agricolae, |
| 126 | 128 |
BiocFileCache, |
| 127 | 129 |
BiocStyle, |
J Wokaty authored on 01/11/2022 15:21:15
J Wokaty authored on 01/11/2022 15:21:15
Nitesh Turaga authored on 26/04/2022 16:02:16
Nitesh Turaga authored on 26/04/2022 16:02:16
+ update news
+ add citation file
Gavin Rhys Lloyd authored on 28/02/2022 14:27:17
| ... | ... |
@@ -1,19 +1,21 @@ |
| 1 | 1 |
Package: structToolbox |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Data processing & analysis tools for Metabolomics and other omics |
| 4 |
-Version: 1.7.1 |
|
| 4 |
+Version: 1.7.2 |
|
| 5 | 5 |
Authors@R: c( |
| 6 | 6 |
person( |
| 7 | 7 |
c("Gavin","Rhys"),
|
| 8 | 8 |
"Lloyd", |
| 9 | 9 |
role=c("aut","cre"),
|
| 10 |
- email="[email protected]"), |
|
| 10 |
+ email="[email protected]", |
|
| 11 |
+ comment = c(ORCID = "0000-0001-7989-6695") |
|
| 12 |
+ ), |
|
| 11 | 13 |
person( |
| 12 | 14 |
c("Ralf","Johannes", "Maria"),
|
| 13 | 15 |
"Weber", |
| 14 | 16 |
role=c("aut"),
|
| 15 | 17 |
email="[email protected]") |
| 16 |
- ) |
|
| 18 |
+ ) |
|
| 17 | 19 |
Description: An extensive set of data (pre-)processing and analysis methods and |
| 18 | 20 |
tools for metabolomics and other omics, with a strong emphasis on statistics and |
| 19 | 21 |
machine learning. This toolbox allows the user to build extensive and |
* add selectivity ratio
* replace vip_summary with feature_importance
renamed and now allows vip, sr and sr_pvalues to be plotted
* add equal_split model
random subsets so generate training sets with equal group numbers
* plot 1 - p-value
to conform with the "best" feature being a maximum value
* add resample iterator
subsample at random over a number of iterations. Option to use
different kinds of splitting methods. Corresponding chart.
* allow use of list() for factor_name
* force apply not to simplify output to guarantee returning a list
* update example
* add correct parameter
collect will collect the requested model output over all iterations in a list WORK IN PROGRESS
* add collection of multiple outputs of model sequence
* plot reg coeff on rhs
* match outputs of xval for use with grid search etc
* specify levels when converting predictions to factor
* change PLSDA to inherit from PLSR
rename some charts to be compatible with both PLSR and PLSDA
* allow y-block column selection
* re-assign y output after PLSR with factor
* update vignettes wrt PLS changes
* update documentation
* update R version to 4.1
* update documentation
* update documentation
* update scatter plot
- new scatter chart object
- used by PCA scores, PLSR/PLSDA scores
- other charts updated to reflect changes in scores plots where necessary
- added ycol param to plots for when y-block is a matrix
* add url to github
* add plsda scores alias
- plsda_scores_plot and pls_scores_plot do that same thing
Included for backwards compatability
- added components back as parameter for scores plots for backwards compatibility
* fix broken example
* fix broken tests
- scores is now returned as a DatasetExperiment object not a data.frame
* Update data_analysis_omics_using_the_structtoolbox.Rmd
- wrt changes in scores plots
* update documentation
* fix colnames for Y matrix
Gavin Rhys Lloyd authored on 28/02/2022 12:38:08
• GitHub committed on 28/02/2022 12:38:08
| ... | ... |
@@ -40,10 +40,11 @@ Collate: |
| 40 | 40 |
'HSDEM_class.R' |
| 41 | 41 |
'MTBLS79_dataset_class.R' |
| 42 | 42 |
'PCA_class.R' |
| 43 |
+ 'scatter_chart_class.R' |
|
| 43 | 44 |
'PCA_plotfcns.R' |
| 45 |
+ 'PLSR_class.R' |
|
| 44 | 46 |
'PLSDA_class.R' |
| 45 | 47 |
'PLSDA_charts.R' |
| 46 |
- 'PLSR_class.R' |
|
| 47 | 48 |
'as_data_frame_doc.R' |
| 48 | 49 |
'autoscale_class.R' |
| 49 | 50 |
'balanced_accuracy_class.R' |
| ... | ... |
@@ -57,6 +58,8 @@ Collate: |
| 57 | 58 |
'corr_coef_class.R' |
| 58 | 59 |
'd_ratio_filter_class.R' |
| 59 | 60 |
'dataset_chart_classes.R' |
| 61 |
+ 'split_data_class.R' |
|
| 62 |
+ 'equal_split_class.R' |
|
| 60 | 63 |
'factor_barchart_class.R' |
| 61 | 64 |
'feature_plot_array_class.R' |
| 62 | 65 |
'feature_profile_class.R' |
| ... | ... |
@@ -90,14 +93,14 @@ Collate: |
| 90 | 93 |
'paretoscale_class.R' |
| 91 | 94 |
'permutation_test_class.R' |
| 92 | 95 |
'permute_sample_order_class.R' |
| 93 |
- 'plsda_vip_summary_chart.R' |
|
| 96 |
+ 'plsda_feature_significance_chart.R' |
|
| 94 | 97 |
'pqn_norm_method_class.R' |
| 95 | 98 |
'prop_na_class.R' |
| 96 | 99 |
'r_squared_class.R' |
| 100 |
+ 'resample_class.R' |
|
| 97 | 101 |
'rsd_filter.R' |
| 98 | 102 |
'run_doc.R' |
| 99 | 103 |
'sb_corr.R' |
| 100 |
- 'split_data_class.R' |
|
| 101 | 104 |
'stratified_split_class.R' |
| 102 | 105 |
'structToolbox.R' |
| 103 | 106 |
'svm_classifier_class.R' |
| ... | ... |
@@ -140,3 +143,4 @@ Suggests: agricolae, |
| 140 | 143 |
rappdirs |
| 141 | 144 |
VignetteBuilder: knitr |
| 142 | 145 |
biocViews: WorkflowStep, Metabolomics |
| 146 |
+URL: https://github.com/computational-metabolomics/structToolbox |
Gavin Rhys Lloyd authored on 04/02/2022 09:48:26
Nitesh Turaga authored on 26/10/2021 16:57:03
Nitesh Turaga authored on 26/10/2021 16:57:03
Gavin Rhys Lloyd authored on 07/10/2021 12:22:38
Gavin Rhys Lloyd authored on 01/10/2021 16:52:24
| ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: structToolbox |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Data processing & analysis tools for Metabolomics and other omics |
| 4 |
-Version: 1.5.5 |
|
| 4 |
+Version: 1.5.6 |
|
| 5 | 5 |
Authors@R: c( |
| 6 | 6 |
person( |
| 7 | 7 |
c("Gavin","Rhys"),
|
| ... | ... |
@@ -116,7 +116,7 @@ Imports: ggplot2, |
| 116 | 116 |
sp, |
| 117 | 117 |
stats, |
| 118 | 118 |
utils |
| 119 |
-RoxygenNote: 7.1.1 |
|
| 119 |
+RoxygenNote: 7.1.2 |
|
| 120 | 120 |
Suggests: agricolae, |
| 121 | 121 |
BiocFileCache, |
| 122 | 122 |
BiocStyle, |
in particular for paired tests, where additional features might be excluded
Gavin Rhys Lloyd authored on 08/09/2021 11:29:50
Gavin Rhys Lloyd authored on 24/08/2021 08:42:24
Gavin Rhys Lloyd authored on 30/07/2021 20:06:29
Gavin Rhys Lloyd authored on 26/07/2021 09:30:25
• GitHub committed on 26/07/2021 09:30:25
| ... | ... |
@@ -29,11 +29,11 @@ Description: An extensive set of data (pre-)processing and analysis methods and |
| 29 | 29 |
standardised definitions for the different methods, inputs and outputs. |
| 30 | 30 |
License: GPL-3 |
| 31 | 31 |
Encoding: UTF-8 |
| 32 |
-LazyData: true |
|
| 33 | 32 |
Collate: |
| 34 | 33 |
'AUC_metric_class.R' |
| 35 | 34 |
'entity_objects.R' |
| 36 | 35 |
'DFA_class.R' |
| 36 |
+ 'zzz.R' |
|
| 37 | 37 |
'anova_class.R' |
| 38 | 38 |
'HSD_class.R' |
| 39 | 39 |
'mixed_effect_class.R' |
| ... | ... |
@@ -106,8 +106,7 @@ Collate: |
| 106 | 106 |
'ttest_class.R' |
| 107 | 107 |
'vec_norm_class.R' |
| 108 | 108 |
'wilcox_test_class.R' |
| 109 |
- 'zzz.R' |
|
| 110 |
-Depends: R (>= 4.0), struct (>= 1.4.0) |
|
| 109 |
+Depends: R (>= 4.0), struct (>= 1.5.1) |
|
| 111 | 110 |
Imports: ggplot2, |
| 112 | 111 |
ggthemes, |
| 113 | 112 |
grid, |
| ... | ... |
@@ -137,6 +136,7 @@ Suggests: agricolae, |
| 137 | 136 |
ropls, |
| 138 | 137 |
rmarkdown, |
| 139 | 138 |
Rtsne, |
| 140 |
- testthat |
|
| 139 |
+ testthat, |
|
| 140 |
+ rappdirs |
|
| 141 | 141 |
VignetteBuilder: knitr |
| 142 | 142 |
biocViews: WorkflowStep, Metabolomics |
Gavin Rhys Lloyd authored on 07/07/2021 09:29:33
• GitHub committed on 07/07/2021 09:29:33
| ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: structToolbox |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Data processing & analysis tools for Metabolomics and other omics |
| 4 |
-Version: 1.5.1 |
|
| 4 |
+Version: 1.5.2 |
|
| 5 | 5 |
Authors@R: c( |
| 6 | 6 |
person( |
| 7 | 7 |
c("Gavin","Rhys"),
|
| ... | ... |
@@ -107,7 +107,7 @@ Collate: |
| 107 | 107 |
'vec_norm_class.R' |
| 108 | 108 |
'wilcox_test_class.R' |
| 109 | 109 |
'zzz.R' |
| 110 |
-Depends: R (>= 4.0), struct (>= 1.2.0) |
|
| 110 |
+Depends: R (>= 4.0), struct (>= 1.4.0) |
|
| 111 | 111 |
Imports: ggplot2, |
| 112 | 112 |
ggthemes, |
| 113 | 113 |
grid, |
* fix paired ttest/wilcoxon test
rownames must be kept in sync for data and meta data of SummarizedExperiment type objects
Gavin Rhys Lloyd authored on 25/06/2021 12:52:31
• GitHub committed on 25/06/2021 12:52:31
Nitesh Turaga authored on 19/05/2021 16:49:11
Nitesh Turaga authored on 19/05/2021 16:49:11
ready for v1.4.0 bioc 3.13 release
Gavin Rhys Lloyd authored on 11/05/2021 11:46:41
Gavin Rhys Lloyd authored on 11/05/2021 10:28:24
- allow norm or t distributed ellipses
- allow changing confidence level
Gavin Rhys Lloyd authored on 29/04/2021 13:48:42
Gavin Rhys Lloyd authored on 28/04/2021 12:21:01
Gavin Rhys Lloyd authored on 26/04/2021 16:48:03
Gavin Rhys Lloyd authored on 29/03/2021 08:07:44
• GitHub committed on 29/03/2021 08:07:44
Gavin Rhys Lloyd authored on 26/02/2021 12:03:16
• GitHub committed on 26/02/2021 12:03:16
Gavin Rhys Lloyd authored on 25/02/2021 18:55:54
• GitHub committed on 25/02/2021 18:55:54
* fix base=10 regardless of input (see #15)
class constructor was always setting base to 10 instead of the input value
* bug fix issue #7
Correctly re-order the sample_meta column for colouring samples in the dendrogram plot
* fix for https://github.com/computational-metabolomics/structToolbox/issues/18 (#20)
correctly reorder the factor labels so that the control group always ends up in the denominator for the fold change calculation.
* fix for https://github.com/computational-metabolomics/structToolbox/issues/18
fixed incorrect length check on matching class labels.
* Issue 17 ttest factor (#21)
* convert to factor if not one already
fix for issue #17
* update roxygen version
* fix for issue #9 (#22)
changed from lapply to vapply and used drop=FALSE to ensure compatibility with a single factor.
* allow user to set lambda (#24)
- lambda changed to input parameter. NULL = uses pmp optimisation
- model_predict now uses the set value of lambda, or lambda_opt if used.
- documentation updated
* Feature non parametric fold change (#26)
* add "median" method
based on DOI: 10.1080/00949650212140 can now calcuate fold changes equivalent to using medians and corresponding confidence intervals
* use wilcox for paired median intervals
make use of wilcox.test to estimate intervals for the median when using median for paired samples
* Issue 23 filter by name (#27)
moved all model_apply functionality to model_predict so that model_train and model_predict can be used as well as model_apply
* Update mean_of_medians.R (#29)
* fix for #28
- correctly loop over all levels in the named factor
* update documentation
Description and inputs now pulled from the object definitions for consistency.
* fix definition of label_features
allows NULL and description updated
* add feature_profile_array chart
Gavin Rhys Lloyd authored on 23/02/2021 14:02:23
• GitHub committed on 23/02/2021 14:02:23
| ... | ... |
@@ -58,6 +58,7 @@ Collate: |
| 58 | 58 |
'd_ratio_filter_class.R' |
| 59 | 59 |
'dataset_chart_classes.R' |
| 60 | 60 |
'factor_barchart_class.R' |
| 61 |
+ 'feature_plot_array_class.R' |
|
| 61 | 62 |
'feature_profile_class.R' |
| 62 | 63 |
'filter_by_name_class.R' |
| 63 | 64 |
'filter_na_count.R' |
| ... | ... |
@@ -104,7 +105,7 @@ Collate: |
| 104 | 105 |
'vec_norm_class.R' |
| 105 | 106 |
'wilcox_test_class.R' |
| 106 | 107 |
'zzz.R' |
| 107 |
-Depends: R (>= 4.0), struct (>= 1.1.2) |
|
| 108 |
+Depends: R (>= 4.0), struct (>= 1.2.0) |
|
| 108 | 109 |
Imports: ggplot2, |
| 109 | 110 |
ggthemes, |
| 110 | 111 |
grid, |
Nitesh Turaga authored on 27/10/2020 15:53:02
Nitesh Turaga authored on 27/10/2020 15:53:02
* fix base=10 regardless of input (see #15)
class constructor was always setting base to 10 instead of the input value
* merge bug fix 1.01 into dev (#19)
* bug fix issue #7
Correctly re-order the sample_meta column for colouring samples in the dendrogram plot
* version bump
bug fix issue #7
* fix for https://github.com/computational-metabolomics/structToolbox/issues/18 (#20)
correctly reorder the factor labels so that the control group always ends up in the denominator for the fold change calculation.
* fix for https://github.com/computational-metabolomics/structToolbox/issues/18
fixed incorrect length check on matching class labels.
* Issue 17 ttest factor (#21)
* convert to factor if not one already
fix for issue #17
* update roxygen version
* fix for issue #9 (#22)
changed from lapply to vapply and used drop=FALSE to ensure compatibility with a single factor.
* allow user to set lambda (#24)
- lambda changed to input parameter. NULL = uses pmp optimisation
- model_predict now uses the set value of lambda, or lambda_opt if used.
- documentation updated
* Feature non parametric fold change (#26)
* add "median" method
based on DOI: 10.1080/00949650212140 can now calcuate fold changes equivalent to using medians and corresponding confidence intervals
* update documentation
* update median method
now correctly calculates ratio of medians
* use wilcox for paired median intervals
make use of wilcox.test to estimate intervals for the median when using median for paired samples
* Issue 23 filter by name (#27)
* fix for #23
moved all model_apply functionality to model_predict so that model_train and model_predict can be used as well as model_apply
* update documentation
* Update mean_of_medians.R (#29)
fix for #28
- correctly loop over all levels in the named factor
* Feature documentation 3 12 (#31)
* update documentation
Description and inputs now pulled from the object definitions for consistency.
* fix definition of label_features
allows NULL and description updated
* replace non ascii characters
* export mixed_effect object
* use correct object name to generate documentation
* export mixed_effect object
* remove non ascii characters
* update tests with new object name
* add import for capture.output
* add import for capture.output
* use pca_biplot in tests
chart was renamed
* add utils import
* update struct dependency version
* update documentation
* update news, version bump
Gavin Rhys Lloyd authored on 25/10/2020 08:50:13
• GitHub committed on 25/10/2020 08:50:13
| ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: structToolbox |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Data processing & analysis tools for Metabolomics and other omics |
| 4 |
-Version: 1.1.1 |
|
| 4 |
+Version: 1.1.2 |
|
| 5 | 5 |
Authors@R: c( |
| 6 | 6 |
person( |
| 7 | 7 |
c("Gavin","Rhys"),
|
| ... | ... |
@@ -104,7 +104,7 @@ Collate: |
| 104 | 104 |
'vec_norm_class.R' |
| 105 | 105 |
'wilcox_test_class.R' |
| 106 | 106 |
'zzz.R' |
| 107 |
-Depends: R (>= 4.0), struct (>= 0.99.10) |
|
| 107 |
+Depends: R (>= 4.0), struct (>= 1.1.2) |
|
| 108 | 108 |
Imports: ggplot2, |
| 109 | 109 |
ggthemes, |
| 110 | 110 |
grid, |
| ... | ... |
@@ -112,8 +112,9 @@ Imports: ggplot2, |
| 112 | 112 |
methods, |
| 113 | 113 |
scales, |
| 114 | 114 |
sp, |
| 115 |
- stats |
|
| 116 |
-RoxygenNote: 7.1.0 |
|
| 115 |
+ stats, |
|
| 116 |
+ utils |
|
| 117 |
+RoxygenNote: 7.1.1 |
|
| 117 | 118 |
Suggests: agricolae, |
| 118 | 119 |
BiocFileCache, |
| 119 | 120 |
BiocStyle, |
Nitesh Turaga authored on 27/04/2020 19:33:37
Nitesh Turaga authored on 27/04/2020 19:33:37
Gavin Rhys Lloyd authored on 24/04/2020 19:40:35
| ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: structToolbox |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Data processing & analysis tools for Metabolomics and other omics |
| 4 |
-Version: 0.99.9 |
|
| 4 |
+Version: 0.99.10 |
|
| 5 | 5 |
Authors@R: c( |
| 6 | 6 |
person( |
| 7 | 7 |
c("Gavin","Rhys"),
|
| ... | ... |
@@ -135,4 +135,4 @@ Suggests: agricolae, |
| 135 | 135 |
Rtsne, |
| 136 | 136 |
testthat |
| 137 | 137 |
VignetteBuilder: knitr |
| 138 |
-biocViews: WorkflowStep |
|
| 138 |
+biocViews: WorkflowStep, Metabolomics |
Gavin Rhys Lloyd authored on 23/04/2020 18:27:21
Gavin Rhys Lloyd authored on 22/04/2020 20:14:46
| ... | ... |
@@ -14,10 +14,19 @@ Authors@R: c( |
| 14 | 14 |
role=c("aut"),
|
| 15 | 15 |
email="[email protected]") |
| 16 | 16 |
) |
| 17 |
-Description: Extends the class templates provided by the struct package to |
|
| 18 |
- provide PCA, PLS models with cross-validation, permutation testing etc. Also |
|
| 19 |
- includes a suite of univariate tests and data processing models for building |
|
| 20 |
- complete workflows. |
|
| 17 |
+Description: An extensive set of data (pre-)processing and analysis methods and |
|
| 18 |
+ tools for metabolomics and other omics, with a strong emphasis on statistics and |
|
| 19 |
+ machine learning. This toolbox allows the user to build extensive and |
|
| 20 |
+ standardised workflows for data analysis. The methods and tools have been |
|
| 21 |
+ implemented using class-based templates provided by the struct (Statistics |
|
| 22 |
+ in R Using Class-based Templates) package. The toolbox includes pre-processing |
|
| 23 |
+ methods (e.g. signal drift and batch correction, normalisation, missing value |
|
| 24 |
+ imputation and scaling), univariate (e.g. ttest, various forms of ANOVA, |
|
| 25 |
+ Kruskal–Wallis test and more) and multivariate statistical methods (e.g. PCA and |
|
| 26 |
+ PLS, including cross-validation and permutation testing) as well as machine |
|
| 27 |
+ learning methods (e.g. Support Vector Machines). The |
|
| 28 |
+ STATistics Ontology (STATO) has been integrated and implemented to provide |
|
| 29 |
+ standardised definitions for the different methods, inputs and outputs. |
|
| 21 | 30 |
License: GPL-3 |
| 22 | 31 |
Encoding: UTF-8 |
| 23 | 32 |
LazyData: true |
Gavin Rhys Lloyd authored on 22/04/2020 20:09:30
| ... | ... |
@@ -1,9 +1,19 @@ |
| 1 | 1 |
Package: structToolbox |
| 2 | 2 |
Type: Package |
| 3 |
-Title: Some tools bult using the struct package |
|
| 4 |
-Version: 0.99.8 |
|
| 5 |
-Author: Gavin Rhys Lloyd |
|
| 6 |
-Maintainer: Gavin Rhys Lloyd <[email protected]> |
|
| 3 |
+Title: Data processing & analysis tools for Metabolomics and other omics |
|
| 4 |
+Version: 0.99.9 |
|
| 5 |
+Authors@R: c( |
|
| 6 |
+ person( |
|
| 7 |
+ c("Gavin","Rhys"),
|
|
| 8 |
+ "Lloyd", |
|
| 9 |
+ role=c("aut","cre"),
|
|
| 10 |
+ email="[email protected]"), |
|
| 11 |
+ person( |
|
| 12 |
+ c("Ralf","Johannes", "Maria"),
|
|
| 13 |
+ "Weber", |
|
| 14 |
+ role=c("aut"),
|
|
| 15 |
+ email="[email protected]") |
|
| 16 |
+ ) |
|
| 7 | 17 |
Description: Extends the class templates provided by the struct package to |
| 8 | 18 |
provide PCA, PLS models with cross-validation, permutation testing etc. Also |
| 9 | 19 |
includes a suite of univariate tests and data processing models for building |
| ... | ... |
@@ -58,6 +68,7 @@ Collate: |
| 58 | 68 |
'linear_model_class.R' |
| 59 | 69 |
'log_transform.R' |
| 60 | 70 |
'mean_centre_class.R' |
| 71 |
+ 'mean_of_medians.R' |
|
| 61 | 72 |
'model_apply_doc.R' |
| 62 | 73 |
'model_predict_doc.R' |
| 63 | 74 |
'model_reverse_doc.R' |
| ... | ... |
@@ -95,6 +106,7 @@ Imports: ggplot2, |
| 95 | 106 |
stats |
| 96 | 107 |
RoxygenNote: 7.1.0 |
| 97 | 108 |
Suggests: agricolae, |
| 109 |
+ BiocFileCache, |
|
| 98 | 110 |
BiocStyle, |
| 99 | 111 |
car, |
| 100 | 112 |
covr, |
+ AUC metric
+ PLS charts (reg coeff, ROC, VIP scores)
+ stratified data set splitting
Gavin Rhys Lloyd authored on 07/04/2020 14:39:32
| ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: structToolbox |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Some tools bult using the struct package |
| 4 |
-Version: 0.99.7 |
|
| 4 |
+Version: 0.99.8 |
|
| 5 | 5 |
Author: Gavin Rhys Lloyd |
| 6 | 6 |
Maintainer: Gavin Rhys Lloyd <[email protected]> |
| 7 | 7 |
Description: Extends the class templates provided by the struct package to |
| ... | ... |
@@ -12,6 +12,7 @@ License: GPL-3 |
| 12 | 12 |
Encoding: UTF-8 |
| 13 | 13 |
LazyData: true |
| 14 | 14 |
Collate: |
| 15 |
+ 'AUC_metric_class.R' |
|
| 15 | 16 |
'entity_objects.R' |
| 16 | 17 |
'DFA_class.R' |
| 17 | 18 |
'anova_class.R' |
| ... | ... |
@@ -75,6 +76,7 @@ Collate: |
| 75 | 76 |
'run_doc.R' |
| 76 | 77 |
'sb_corr.R' |
| 77 | 78 |
'split_data_class.R' |
| 79 |
+ 'stratified_split_class.R' |
|
| 78 | 80 |
'structToolbox.R' |
| 79 | 81 |
'svm_classifier_class.R' |
| 80 | 82 |
'tSNE_class.R' |
| ... | ... |
@@ -103,6 +105,7 @@ Suggests: agricolae, |
| 103 | 105 |
knitr, |
| 104 | 106 |
magick, |
| 105 | 107 |
nlme, |
| 108 |
+ openxlsx, |
|
| 106 | 109 |
pls, |
| 107 | 110 |
pmp, |
| 108 | 111 |
reshape2, |
Gavin Rhys Lloyd authored on 23/03/2020 13:54:11
| ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: structToolbox |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Some tools bult using the struct package |
| 4 |
-Version: 0.99.6 |
|
| 4 |
+Version: 0.99.7 |
|
| 5 | 5 |
Author: Gavin Rhys Lloyd |
| 6 | 6 |
Maintainer: Gavin Rhys Lloyd <[email protected]> |
| 7 | 7 |
Description: Extends the class templates provided by the struct package to |
Gavin Rhys Lloyd authored on 20/03/2020 16:10:06
| ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: structToolbox |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Some tools bult using the struct package |
| 4 |
-Version: 0.99.5 |
|
| 4 |
+Version: 0.99.6 |
|
| 5 | 5 |
Author: Gavin Rhys Lloyd |
| 6 | 6 |
Maintainer: Gavin Rhys Lloyd <[email protected]> |
| 7 | 7 |
Description: Extends the class templates provided by the struct package to |
| ... | ... |
@@ -91,7 +91,7 @@ Imports: ggplot2, |
| 91 | 91 |
scales, |
| 92 | 92 |
sp, |
| 93 | 93 |
stats |
| 94 |
-RoxygenNote: 7.0.2 |
|
| 94 |
+RoxygenNote: 7.1.0 |
|
| 95 | 95 |
Suggests: agricolae, |
| 96 | 96 |
BiocStyle, |
| 97 | 97 |
car, |
Gavin Rhys Lloyd authored on 17/03/2020 11:25:59
Gavin Rhys Lloyd authored on 16/03/2020 16:15:00
| ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: structToolbox |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Some tools bult using the struct package |
| 4 |
-Version: 0.99.4 |
|
| 4 |
+Version: 0.99.5 |
|
| 5 | 5 |
Author: Gavin Rhys Lloyd |
| 6 | 6 |
Maintainer: Gavin Rhys Lloyd <[email protected]> |
| 7 | 7 |
Description: Extends the class templates provided by the struct package to |
| ... | ... |
@@ -13,6 +13,7 @@ Encoding: UTF-8 |
| 13 | 13 |
LazyData: true |
| 14 | 14 |
Collate: |
| 15 | 15 |
'entity_objects.R' |
| 16 |
+ 'DFA_class.R' |
|
| 16 | 17 |
'anova_class.R' |
| 17 | 18 |
'HSD_class.R' |
| 18 | 19 |
'mixed_effect_class.R' |
Gavin Rhys Lloyd authored on 06/03/2020 15:08:01
• GitHub committed on 06/03/2020 15:08:01
| ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: structToolbox |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Some tools bult using the struct package |
| 4 |
-Version: 0.99.3 |
|
| 4 |
+Version: 0.99.4 |
|
| 5 | 5 |
Author: Gavin Rhys Lloyd |
| 6 | 6 |
Maintainer: Gavin Rhys Lloyd <[email protected]> |
| 7 | 7 |
Description: Extends the class templates provided by the struct package to |
Gavin Rhys Lloyd authored on 06/03/2020 15:00:54
| ... | ... |
@@ -95,6 +95,8 @@ Suggests: agricolae, |
| 95 | 95 |
BiocStyle, |
| 96 | 96 |
car, |
| 97 | 97 |
covr, |
| 98 |
+ cowplot, |
|
| 99 |
+ e1071, |
|
| 98 | 100 |
emmeans, |
| 99 | 101 |
ggdendro, |
| 100 | 102 |
knitr, |
| ... | ... |
@@ -103,6 +105,7 @@ Suggests: agricolae, |
| 103 | 105 |
pls, |
| 104 | 106 |
pmp, |
| 105 | 107 |
reshape2, |
| 108 |
+ ropls, |
|
| 106 | 109 |
rmarkdown, |
| 107 | 110 |
Rtsne, |
| 108 | 111 |
testthat |
| ... | ... |
@@ -32,6 +32,7 @@ Collate: |
| 32 | 32 |
'chart_plot_doc.R' |
| 33 | 33 |
'classical_lsq_class.R' |
| 34 | 34 |
'confounders_clsq_class.R' |
| 35 |
+ 'constant_sum_norm_class.R' |
|
| 35 | 36 |
'corr_coef_class.R' |
| 36 | 37 |
'd_ratio_filter_class.R' |
| 37 | 38 |
'dataset_chart_classes.R' |
| ... | ... |
@@ -61,6 +62,7 @@ Collate: |
| 61 | 62 |
'model_train_doc.R' |
| 62 | 63 |
'mv_feature_filter_class.R' |
| 63 | 64 |
'mv_sample_filter_class.R' |
| 65 |
+ 'nroot_transform_class.R' |
|
| 64 | 66 |
'pairs_filter_class.R' |
| 65 | 67 |
'paretoscale_class.R' |
| 66 | 68 |
'permutation_test_class.R' |
| ... | ... |
@@ -73,6 +75,7 @@ Collate: |
| 73 | 75 |
'sb_corr.R' |
| 74 | 76 |
'split_data_class.R' |
| 75 | 77 |
'structToolbox.R' |
| 78 |
+ 'svm_classifier_class.R' |
|
| 76 | 79 |
'tSNE_class.R' |
| 77 | 80 |
'ttest_class.R' |
| 78 | 81 |
'vec_norm_class.R' |
package version increased to 0.99.3
struct version increased to 0.99.5
Gavin Rhys Lloyd authored on 24/02/2020 11:41:47
| ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: structToolbox |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Some tools bult using the struct package |
| 4 |
-Version: 0.99.2 |
|
| 4 |
+Version: 0.99.3 |
|
| 5 | 5 |
Author: Gavin Rhys Lloyd |
| 6 | 6 |
Maintainer: Gavin Rhys Lloyd <[email protected]> |
| 7 | 7 |
Description: Extends the class templates provided by the struct package to |
| ... | ... |
@@ -78,7 +78,7 @@ Collate: |
| 78 | 78 |
'vec_norm_class.R' |
| 79 | 79 |
'wilcox_test_class.R' |
| 80 | 80 |
'zzz.R' |
| 81 |
-Depends: R (>= 4.0), struct (>= 0.99.4) |
|
| 81 |
+Depends: R (>= 4.0), struct (>= 0.99.5) |
|
| 82 | 82 |
Imports: ggplot2, |
| 83 | 83 |
ggthemes, |
| 84 | 84 |
grid, |
Gavin Rhys Lloyd authored on 11/02/2020 13:19:28
| ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: structToolbox |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Some tools bult using the struct package |
| 4 |
-Version: 0.99.1 |
|
| 4 |
+Version: 0.99.2 |
|
| 5 | 5 |
Author: Gavin Rhys Lloyd |
| 6 | 6 |
Maintainer: Gavin Rhys Lloyd <[email protected]> |
| 7 | 7 |
Description: Extends the class templates provided by the struct package to |
| ... | ... |
@@ -17,6 +17,7 @@ Collate: |
| 17 | 17 |
'HSD_class.R' |
| 18 | 18 |
'mixed_effect_class.R' |
| 19 | 19 |
'HSDEM_class.R' |
| 20 |
+ 'MTBLS79_dataset_class.R' |
|
| 20 | 21 |
'PCA_class.R' |
| 21 | 22 |
'PCA_plotfcns.R' |
| 22 | 23 |
'PLSDA_class.R' |
| ... | ... |
@@ -70,7 +71,6 @@ Collate: |
| 70 | 71 |
'rsd_filter.R' |
| 71 | 72 |
'run_doc.R' |
| 72 | 73 |
'sb_corr.R' |
| 73 |
- 'sbcms_dataset_class.R' |
|
| 74 | 74 |
'split_data_class.R' |
| 75 | 75 |
'structToolbox.R' |
| 76 | 76 |
'tSNE_class.R' |
Gavin Rhys Lloyd authored on 07/02/2020 17:41:08
| ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: structToolbox |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Some tools bult using the struct package |
| 4 |
-Version: 0.99.0 |
|
| 4 |
+Version: 0.99.1 |
|
| 5 | 5 |
Author: Gavin Rhys Lloyd |
| 6 | 6 |
Maintainer: Gavin Rhys Lloyd <[email protected]> |
| 7 | 7 |
Description: Extends the class templates provided by the struct package to |
Gavin Rhys Lloyd authored on 07/02/2020 17:40:34
Gavin Rhys Lloyd authored on 07/02/2020 17:02:22
| ... | ... |
@@ -1,10 +1,13 @@ |
| 1 | 1 |
Package: structToolbox |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Some tools bult using the struct package |
| 4 |
-Version: 0.8.3 |
|
| 4 |
+Version: 0.99.0 |
|
| 5 | 5 |
Author: Gavin Rhys Lloyd |
| 6 | 6 |
Maintainer: Gavin Rhys Lloyd <[email protected]> |
| 7 |
-Description: Extends the class templates provided by the struct package to provide methods for training PCA, PLS models with cross-validation, permutation testing etc. |
|
| 7 |
+Description: Extends the class templates provided by the struct package to |
|
| 8 |
+ provide PCA, PLS models with cross-validation, permutation testing etc. Also |
|
| 9 |
+ includes a suite of univariate tests and data processing models for building |
|
| 10 |
+ complete workflows. |
|
| 8 | 11 |
License: GPL-3 |
| 9 | 12 |
Encoding: UTF-8 |
| 10 | 13 |
LazyData: true |
| ... | ... |
@@ -19,6 +22,7 @@ Collate: |
| 19 | 22 |
'PLSDA_class.R' |
| 20 | 23 |
'PLSDA_charts.R' |
| 21 | 24 |
'PLSR_class.R' |
| 25 |
+ 'as_data_frame_doc.R' |
|
| 22 | 26 |
'autoscale_class.R' |
| 23 | 27 |
'balanced_accuracy_class.R' |
| 24 | 28 |
'blank_filter_class.R' |
| ... | ... |
@@ -74,9 +78,8 @@ Collate: |
| 74 | 78 |
'vec_norm_class.R' |
| 75 | 79 |
'wilcox_test_class.R' |
| 76 | 80 |
'zzz.R' |
| 77 |
-Depends: struct (>= 0.99.3) |
|
| 78 |
-Imports: datasets, |
|
| 79 |
- ggplot2, |
|
| 81 |
+Depends: struct (>= 0.99.4) |
|
| 82 |
+Imports: ggplot2, |
|
| 80 | 83 |
ggthemes, |
| 81 | 84 |
grid, |
| 82 | 85 |
gridExtra, |
| ... | ... |
@@ -90,11 +93,12 @@ Suggests: agricolae, |
| 90 | 93 |
car, |
| 91 | 94 |
covr, |
| 92 | 95 |
emmeans, |
| 93 |
- pmp, |
|
| 94 | 96 |
ggdendro, |
| 95 | 97 |
knitr, |
| 98 |
+ magick, |
|
| 96 | 99 |
nlme, |
| 97 | 100 |
pls, |
| 101 |
+ pmp, |
|
| 98 | 102 |
reshape2, |
| 99 | 103 |
rmarkdown, |
| 100 | 104 |
Rtsne, |
Gavin Rhys Lloyd authored on 07/02/2020 09:54:30
| ... | ... |
@@ -75,30 +75,29 @@ Collate: |
| 75 | 75 |
'wilcox_test_class.R' |
| 76 | 76 |
'zzz.R' |
| 77 | 77 |
Depends: struct (>= 0.99.3) |
| 78 |
-Imports: ggplot2, |
|
| 79 |
- pmp, |
|
| 80 |
- gridExtra, |
|
| 81 |
- sp, |
|
| 82 |
- scales, |
|
| 83 |
- stats, |
|
| 84 |
- methods, |
|
| 78 |
+Imports: datasets, |
|
| 79 |
+ ggplot2, |
|
| 80 |
+ ggthemes, |
|
| 81 |
+ grid, |
|
| 82 |
+ gridExtra, |
|
| 83 |
+ methods, |
|
| 84 |
+ scales, |
|
| 85 |
+ sp, |
|
| 86 |
+ stats |
|
| 87 |
+RoxygenNote: 7.0.2 |
|
| 88 |
+Suggests: agricolae, |
|
| 89 |
+ BiocStyle, |
|
| 85 | 90 |
car, |
| 86 |
- grid, |
|
| 87 |
- reshape2, |
|
| 88 |
- agricolae, |
|
| 91 |
+ covr, |
|
| 89 | 92 |
emmeans, |
| 90 |
- nlme, |
|
| 91 |
- ggthemes, |
|
| 93 |
+ pmp, |
|
| 92 | 94 |
ggdendro, |
| 93 |
- datasets |
|
| 94 |
-RoxygenNote: 7.0.2 |
|
| 95 |
-Suggests: |
|
| 96 |
- testthat, |
|
| 97 |
- covr, |
|
| 98 | 95 |
knitr, |
| 99 |
- rmarkdown, |
|
| 100 |
- BiocStyle, |
|
| 96 |
+ nlme, |
|
| 101 | 97 |
pls, |
| 102 |
- Rtsne |
|
| 98 |
+ reshape2, |
|
| 99 |
+ rmarkdown, |
|
| 100 |
+ Rtsne, |
|
| 101 |
+ testthat |
|
| 103 | 102 |
VignetteBuilder: knitr |
| 104 | 103 |
biocViews: WorkflowStep |
Gavin Rhys Lloyd authored on 06/02/2020 13:51:52
| ... | ... |
@@ -18,8 +18,6 @@ Collate: |
| 18 | 18 |
'PCA_plotfcns.R' |
| 19 | 19 |
'PLSDA_class.R' |
| 20 | 20 |
'PLSDA_charts.R' |
| 21 |
- 'fold_change_class.R' |
|
| 22 |
- 'PLSFC_class.R' |
|
| 23 | 21 |
'PLSR_class.R' |
| 24 | 22 |
'autoscale_class.R' |
| 25 | 23 |
'balanced_accuracy_class.R' |
| ... | ... |
@@ -38,6 +36,7 @@ Collate: |
| 38 | 36 |
'filter_na_count.R' |
| 39 | 37 |
'filter_smeta_class.R' |
| 40 | 38 |
'fisher_exact_class.R' |
| 39 |
+ 'fold_change_class.R' |
|
| 41 | 40 |
'fold_change_int_class.R' |
| 42 | 41 |
'forward_selection_by_rank_class.R' |
| 43 | 42 |
'ggplot_theme_pub.R' |
| ... | ... |
@@ -59,7 +58,6 @@ Collate: |
| 59 | 58 |
'mv_sample_filter_class.R' |
| 60 | 59 |
'pairs_filter_class.R' |
| 61 | 60 |
'paretoscale_class.R' |
| 62 |
- 'permutation_test2_class.R' |
|
| 63 | 61 |
'permutation_test_class.R' |
| 64 | 62 |
'permute_sample_order_class.R' |
| 65 | 63 |
'pqn_norm_method_class.R' |
Gavin Rhys Lloyd authored on 04/02/2020 10:21:36
| ... | ... |
@@ -76,7 +76,7 @@ Collate: |
| 76 | 76 |
'vec_norm_class.R' |
| 77 | 77 |
'wilcox_test_class.R' |
| 78 | 78 |
'zzz.R' |
| 79 |
-Depends: struct (>= 0.99.2) |
|
| 79 |
+Depends: struct (>= 0.99.3) |
|
| 80 | 80 |
Imports: ggplot2, |
| 81 | 81 |
pmp, |
| 82 | 82 |
gridExtra, |
| ... | ... |
@@ -102,6 +102,5 @@ Suggests: |
| 102 | 102 |
BiocStyle, |
| 103 | 103 |
pls, |
| 104 | 104 |
Rtsne |
| 105 |
-Remotes: computational-metabolomics/struct |
|
| 106 | 105 |
VignetteBuilder: knitr |
| 107 | 106 |
biocViews: WorkflowStep |
Gavin Rhys Lloyd authored on 29/01/2020 16:42:17
sbcms merged into pmp
pmp available on bioconductor
Gavin Rhys Lloyd authored on 29/01/2020 11:52:46
| ... | ... |
@@ -101,10 +101,7 @@ Suggests: |
| 101 | 101 |
rmarkdown, |
| 102 | 102 |
BiocStyle, |
| 103 | 103 |
pls, |
| 104 |
- sbcms, |
|
| 105 | 104 |
Rtsne |
| 106 |
-Remotes: computational-metabolomics/pmp, |
|
| 107 |
- computational-metabolomics/struct, |
|
| 108 |
- computational-metabolomics/sbcms |
|
| 105 |
+Remotes: computational-metabolomics/struct |
|
| 109 | 106 |
VignetteBuilder: knitr |
| 110 | 107 |
biocViews: WorkflowStep |
...temporarily until dependencies become available on bioconductor
Gavin Rhys Lloyd authored on 19/12/2019 15:43:38
| ... | ... |
@@ -103,8 +103,8 @@ Suggests: |
| 103 | 103 |
pls, |
| 104 | 104 |
sbcms, |
| 105 | 105 |
Rtsne |
| 106 |
-Remotes: computational-metabolomics/struct@master, |
|
| 107 |
-computational-metabolomics/pmp, |
|
| 108 |
-computational-metabolomics/sbcms |
|
| 106 |
+Remotes: computational-metabolomics/pmp, |
|
| 107 |
+ computational-metabolomics/struct, |
|
| 108 |
+ computational-metabolomics/sbcms |
|
| 109 | 109 |
VignetteBuilder: knitr |
| 110 | 110 |
biocViews: WorkflowStep |
...temporarily until dependencies become available on biocondutor
Gavin Rhys Lloyd authored on 19/12/2019 15:30:43
changed @param to @slot where appropriate
use DatasetExperiment instead of dataset
merge model and iterator vignette to reduce package size
minor changes to examples due to changes in struct dependency
Gavin Rhys Lloyd authored on 19/12/2019 14:21:40
...rename all function with dot to underscore
replace dataset with DatasetExperiment
Gavin Rhys Lloyd authored on 17/12/2019 15:48:01
| ... | ... |
@@ -76,7 +76,7 @@ Collate: |
| 76 | 76 |
'vec_norm_class.R' |
| 77 | 77 |
'wilcox_test_class.R' |
| 78 | 78 |
'zzz.R' |
| 79 |
-Depends: struct (>= 0.4.1), struct(< 0.5.0) |
|
| 79 |
+Depends: struct (>= 0.99.2) |
|
| 80 | 80 |
Imports: ggplot2, |
| 81 | 81 |
pmp, |
| 82 | 82 |
gridExtra, |
| ... | ... |
@@ -103,8 +103,8 @@ Suggests: |
| 103 | 103 |
pls, |
| 104 | 104 |
sbcms, |
| 105 | 105 |
Rtsne |
| 106 |
-Remotes: computational-metabolomics/pmp, |
|
| 107 |
- computational-metabolomics/[email protected], |
|
| 106 |
+Remotes: computational-metabolomics/[email protected], |
|
| 107 |
+ computational-metabolomics/struct@master, |
|
| 108 | 108 |
computational-metabolomics/sbcms |
| 109 | 109 |
VignetteBuilder: knitr |
| 110 | 110 |
biocViews: WorkflowStep |
Gavin Rhys Lloyd authored on 09/12/2019 10:21:35
Gavin Rhys Lloyd authored on 26/11/2019 14:33:31
pin struct version between 0.4.1 and 0.5.0
Gavin Rhys Lloyd authored on 19/11/2019 09:53:51
| ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: structToolbox |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Some tools bult using the struct package |
| 4 |
-Version: 0.8.2 |
|
| 4 |
+Version: 0.8.3 |
|
| 5 | 5 |
Author: Gavin Rhys Lloyd |
| 6 | 6 |
Maintainer: Gavin Rhys Lloyd <[email protected]> |
| 7 | 7 |
Description: Extends the class templates provided by the struct package to provide methods for training PCA, PLS models with cross-validation, permutation testing etc. |
| ... | ... |
@@ -75,7 +75,7 @@ Collate: |
| 75 | 75 |
'vec_norm_class.R' |
| 76 | 76 |
'wilcox_test_class.R' |
| 77 | 77 |
'zzz.R' |
| 78 |
-Depends: struct (== 0.4.1) |
|
| 78 |
+Depends: struct (>= 0.4.1), struct(< 0.5.0) |
|
| 79 | 79 |
Imports: ggplot2, |
| 80 | 80 |
pmp, |
| 81 | 81 |
gridExtra, |
This reverts commit 128a3495f9b0a02a9ba8711527d1616406485b29.
Gavin Rhys Lloyd authored on 19/11/2019 09:40:22
| ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: structToolbox |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Some tools bult using the struct package |
| 4 |
-Version: 0.8.3 |
|
| 4 |
+Version: 0.8.2 |
|
| 5 | 5 |
Author: Gavin Rhys Lloyd |
| 6 | 6 |
Maintainer: Gavin Rhys Lloyd <[email protected]> |
| 7 | 7 |
Description: Extends the class templates provided by the struct package to provide methods for training PCA, PLS models with cross-validation, permutation testing etc. |
| ... | ... |
@@ -44,7 +44,6 @@ Collate: |
| 44 | 44 |
'glog_class.R' |
| 45 | 45 |
'grid_search_1d_class.R' |
| 46 | 46 |
'hca_class.R' |
| 47 |
- 'kfold_xval2_class.R' |
|
| 48 | 47 |
'kfold_xval_class.R' |
| 49 | 48 |
'kfold_xval_charts.R' |
| 50 | 49 |
'knn_impute_class.R' |
| ... | ... |
@@ -76,7 +75,7 @@ Collate: |
| 76 | 75 |
'vec_norm_class.R' |
| 77 | 76 |
'wilcox_test_class.R' |
| 78 | 77 |
'zzz.R' |
| 79 |
-Depends: struct (>= 0.4.1), struct(< 0.5.0) |
|
| 78 |
+Depends: struct (== 0.4.1) |
|
| 80 | 79 |
Imports: ggplot2, |
| 81 | 80 |
pmp, |
| 82 | 81 |
gridExtra, |
| ... | ... |
@@ -104,7 +103,7 @@ Suggests: |
| 104 | 103 |
sbcms, |
| 105 | 104 |
Rtsne |
| 106 | 105 |
Remotes: computational-metabolomics/pmp, |
| 107 |
- computational-metabolomics/struct, |
|
| 106 |
+ computational-metabolomics/[email protected], |
|
| 108 | 107 |
computational-metabolomics/sbcms |
| 109 | 108 |
VignetteBuilder: knitr |
| 110 | 109 |
biocViews: WorkflowStep |
also force struct version between 0.4.1 and 0.5.0
Gavin Rhys Lloyd authored on 19/11/2019 09:40:14
| ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: structToolbox |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Some tools bult using the struct package |
| 4 |
-Version: 0.8.2 |
|
| 4 |
+Version: 0.8.3 |
|
| 5 | 5 |
Author: Gavin Rhys Lloyd |
| 6 | 6 |
Maintainer: Gavin Rhys Lloyd <[email protected]> |
| 7 | 7 |
Description: Extends the class templates provided by the struct package to provide methods for training PCA, PLS models with cross-validation, permutation testing etc. |
| ... | ... |
@@ -44,6 +44,7 @@ Collate: |
| 44 | 44 |
'glog_class.R' |
| 45 | 45 |
'grid_search_1d_class.R' |
| 46 | 46 |
'hca_class.R' |
| 47 |
+ 'kfold_xval2_class.R' |
|
| 47 | 48 |
'kfold_xval_class.R' |
| 48 | 49 |
'kfold_xval_charts.R' |
| 49 | 50 |
'knn_impute_class.R' |
| ... | ... |
@@ -75,7 +76,7 @@ Collate: |
| 75 | 76 |
'vec_norm_class.R' |
| 76 | 77 |
'wilcox_test_class.R' |
| 77 | 78 |
'zzz.R' |
| 78 |
-Depends: struct (== 0.4.1) |
|
| 79 |
+Depends: struct (>= 0.4.1), struct(< 0.5.0) |
|
| 79 | 80 |
Imports: ggplot2, |
| 80 | 81 |
pmp, |
| 81 | 82 |
gridExtra, |
| ... | ... |
@@ -103,7 +104,7 @@ Suggests: |
| 103 | 104 |
sbcms, |
| 104 | 105 |
Rtsne |
| 105 | 106 |
Remotes: computational-metabolomics/pmp, |
| 106 |
- computational-metabolomics/[email protected], |
|
| 107 |
+ computational-metabolomics/struct, |
|
| 107 | 108 |
computational-metabolomics/sbcms |
| 108 | 109 |
VignetteBuilder: knitr |
| 109 | 110 |
biocViews: WorkflowStep |
fix to allow integer as input for feature_to_plot and number_components
Gavin Rhys Lloyd authored on 12/11/2019 14:44:50
• GitHub committed on 12/11/2019 14:44:50
| ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: structToolbox |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Some tools bult using the struct package |
| 4 |
-Version: 0.8.1 |
|
| 4 |
+Version: 0.8.2 |
|
| 5 | 5 |
Author: Gavin Rhys Lloyd |
| 6 | 6 |
Maintainer: Gavin Rhys Lloyd <[email protected]> |
| 7 | 7 |
Description: Extends the class templates provided by the struct package to provide methods for training PCA, PLS models with cross-validation, permutation testing etc. |
increase required struct version to v0.4.1
Gavin Rhys Lloyd authored on 04/11/2019 11:50:01
• GitHub committed on 04/11/2019 11:50:01
| ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: structToolbox |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Some tools bult using the struct package |
| 4 |
-Version: 0.8.0 |
|
| 4 |
+Version: 0.8.1 |
|
| 5 | 5 |
Author: Gavin Rhys Lloyd |
| 6 | 6 |
Maintainer: Gavin Rhys Lloyd <[email protected]> |
| 7 | 7 |
Description: Extends the class templates provided by the struct package to provide methods for training PCA, PLS models with cross-validation, permutation testing etc. |
| ... | ... |
@@ -75,7 +75,7 @@ Collate: |
| 75 | 75 |
'vec_norm_class.R' |
| 76 | 76 |
'wilcox_test_class.R' |
| 77 | 77 |
'zzz.R' |
| 78 |
-Depends: struct (== 0.4.0) |
|
| 78 |
+Depends: struct (== 0.4.1) |
|
| 79 | 79 |
Imports: ggplot2, |
| 80 | 80 |
pmp, |
| 81 | 81 |
gridExtra, |
| ... | ... |
@@ -103,7 +103,7 @@ Suggests: |
| 103 | 103 |
sbcms, |
| 104 | 104 |
Rtsne |
| 105 | 105 |
Remotes: computational-metabolomics/pmp, |
| 106 |
- computational-metabolomics/[email protected], |
|
| 106 |
+ computational-metabolomics/[email protected], |
|
| 107 | 107 |
computational-metabolomics/sbcms |
| 108 | 108 |
VignetteBuilder: knitr |
| 109 | 109 |
biocViews: WorkflowStep |
Gavin Rhys Lloyd authored on 01/11/2019 13:18:52
• GitHub committed on 01/11/2019 13:18:52
| ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: structToolbox |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Some tools bult using the struct package |
| 4 |
-Version: 0.7.0 |
|
| 4 |
+Version: 0.8.0 |
|
| 5 | 5 |
Author: Gavin Rhys Lloyd |
| 6 | 6 |
Maintainer: Gavin Rhys Lloyd <[email protected]> |
| 7 | 7 |
Description: Extends the class templates provided by the struct package to provide methods for training PCA, PLS models with cross-validation, permutation testing etc. |
Gavin Lloyd (College of Medical and Dental Sciences) authored on 31/10/2019 12:05:28
| ... | ... |
@@ -75,7 +75,7 @@ Collate: |
| 75 | 75 |
'vec_norm_class.R' |
| 76 | 76 |
'wilcox_test_class.R' |
| 77 | 77 |
'zzz.R' |
| 78 |
-Depends: struct |
|
| 78 |
+Depends: struct (== 0.4.0) |
|
| 79 | 79 |
Imports: ggplot2, |
| 80 | 80 |
pmp, |
| 81 | 81 |
gridExtra, |
| ... | ... |
@@ -103,7 +103,7 @@ Suggests: |
| 103 | 103 |
sbcms, |
| 104 | 104 |
Rtsne |
| 105 | 105 |
Remotes: computational-metabolomics/pmp, |
| 106 |
- computational-metabolomics/struct@4bc5702, |
|
| 106 |
+ computational-metabolomics/[email protected], |
|
| 107 | 107 |
computational-metabolomics/sbcms |
| 108 | 108 |
VignetteBuilder: knitr |
| 109 | 109 |
biocViews: WorkflowStep |
Gavin Lloyd (College of Medical and Dental Sciences) authored on 31/10/2019 11:54:39
| ... | ... |
@@ -24,6 +24,7 @@ Collate: |
| 24 | 24 |
'autoscale_class.R' |
| 25 | 25 |
'balanced_accuracy_class.R' |
| 26 | 26 |
'blank_filter_class.R' |
| 27 |
+ 'bootstrap_class.R' |
|
| 27 | 28 |
'calculate_doc.R' |
| 28 | 29 |
'chart_plot_doc.R' |
| 29 | 30 |
'classical_lsq_class.R' |
| ... | ... |
@@ -57,6 +58,7 @@ Collate: |
| 57 | 58 |
'mv_feature_filter_class.R' |
| 58 | 59 |
'mv_sample_filter_class.R' |
| 59 | 60 |
'pairs_filter_class.R' |
| 61 |
+ 'permutation_test2_class.R' |
|
| 60 | 62 |
'permutation_test_class.R' |
| 61 | 63 |
'permute_sample_order_class.R' |
| 62 | 64 |
'pqn_norm_method_class.R' |
grlloyd authored on 14/10/2019 10:07:10
| ... | ... |
@@ -101,7 +101,7 @@ Suggests: |
| 101 | 101 |
sbcms, |
| 102 | 102 |
Rtsne |
| 103 | 103 |
Remotes: computational-metabolomics/pmp, |
| 104 |
- computational-metabolomics/struct#4bc5702, |
|
| 104 |
+ computational-metabolomics/struct@4bc5702, |
|
| 105 | 105 |
computational-metabolomics/sbcms |
| 106 | 106 |
VignetteBuilder: knitr |
| 107 | 107 |
biocViews: WorkflowStep |
grlloyd authored on 14/10/2019 10:00:53
| ... | ... |
@@ -101,7 +101,7 @@ Suggests: |
| 101 | 101 |
sbcms, |
| 102 | 102 |
Rtsne |
| 103 | 103 |
Remotes: computational-metabolomics/pmp, |
| 104 |
- computational-metabolomics/struct, |
|
| 104 |
+ computational-metabolomics/struct#4bc5702, |
|
| 105 | 105 |
computational-metabolomics/sbcms |
| 106 | 106 |
VignetteBuilder: knitr |
| 107 | 107 |
biocViews: WorkflowStep |
moved some dependencies into suggests and have struct check for packages on first use of object instead by populating the libraries slot of objects
Gavin Rhys Lloyd authored on 25/09/2019 17:47:11
| ... | ... |
@@ -77,7 +77,6 @@ Depends: struct |
| 77 | 77 |
Imports: ggplot2, |
| 78 | 78 |
pmp, |
| 79 | 79 |
gridExtra, |
| 80 |
- pls, |
|
| 81 | 80 |
sp, |
| 82 | 81 |
scales, |
| 83 | 82 |
stats, |
| ... | ... |
@@ -90,7 +89,6 @@ Imports: ggplot2, |
| 90 | 89 |
nlme, |
| 91 | 90 |
ggthemes, |
| 92 | 91 |
ggdendro, |
| 93 |
- Rtsne, |
|
| 94 | 92 |
datasets |
| 95 | 93 |
RoxygenNote: 6.1.1 |
| 96 | 94 |
Suggests: |
| ... | ... |
@@ -99,7 +97,9 @@ Suggests: |
| 99 | 97 |
knitr, |
| 100 | 98 |
rmarkdown, |
| 101 | 99 |
BiocStyle, |
| 102 |
- sbcms |
|
| 100 |
+ pls, |
|
| 101 |
+ sbcms, |
|
| 102 |
+ Rtsne |
|
| 103 | 103 |
Remotes: computational-metabolomics/pmp, |
| 104 | 104 |
computational-metabolomics/struct, |
| 105 | 105 |
computational-metabolomics/sbcms |
grlloyd authored on 24/09/2019 13:06:26
grlloyd authored on 24/09/2019 10:02:55
| ... | ... |
@@ -89,7 +89,8 @@ Imports: ggplot2, |
| 89 | 89 |
nlme, |
| 90 | 90 |
ggthemes, |
| 91 | 91 |
ggdendro, |
| 92 |
- Rtsne |
|
| 92 |
+ Rtsne, |
|
| 93 |
+ datasets |
|
| 93 | 94 |
RoxygenNote: 6.1.1 |
| 94 | 95 |
Suggests: |
| 95 | 96 |
testthat, |
| ... | ... |
@@ -99,6 +100,7 @@ Suggests: |
| 99 | 100 |
BiocStyle, |
| 100 | 101 |
sbcms |
| 101 | 102 |
Remotes: computational-metabolomics/pmp, |
| 102 |
- computational-metabolomics/struct |
|
| 103 |
+ computational-metabolomics/struct, |
|
| 104 |
+ computational-metabolomics/sbcms |
|
| 103 | 105 |
VignetteBuilder: knitr |
| 104 | 106 |
biocViews: WorkflowStep |
grlloyd authored on 23/09/2019 15:11:07
grlloyd authored on 23/09/2019 14:26:49
| ... | ... |
@@ -24,6 +24,8 @@ Collate: |
| 24 | 24 |
'autoscale_class.R' |
| 25 | 25 |
'balanced_accuracy_class.R' |
| 26 | 26 |
'blank_filter_class.R' |
| 27 |
+ 'calculate_doc.R' |
|
| 28 |
+ 'chart_plot_doc.R' |
|
| 27 | 29 |
'classical_lsq_class.R' |
| 28 | 30 |
'confounders_clsq_class.R' |
| 29 | 31 |
'corr_coef_class.R' |
| ... | ... |
@@ -48,6 +50,10 @@ Collate: |
| 48 | 50 |
'linear_model_class.R' |
| 49 | 51 |
'log_transform.R' |
| 50 | 52 |
'mean_centre_class.R' |
| 53 |
+ 'model_apply_doc.R' |
|
| 54 |
+ 'model_predict_doc.R' |
|
| 55 |
+ 'model_reverse_doc.R' |
|
| 56 |
+ 'model_train_doc.R' |
|
| 51 | 57 |
'mv_feature_filter_class.R' |
| 52 | 58 |
'mv_sample_filter_class.R' |
| 53 | 59 |
'pairs_filter_class.R' |
| ... | ... |
@@ -57,6 +63,7 @@ Collate: |
| 57 | 63 |
'prop_na_class.R' |
| 58 | 64 |
'r_squared_class.R' |
| 59 | 65 |
'rsd_filter.R' |
| 66 |
+ 'run_doc.R' |
|
| 60 | 67 |
'sb_corr.R' |
| 61 | 68 |
'sbcms_dataset_class.R' |
| 62 | 69 |
'split_data_class.R' |
grlloyd authored on 23/09/2019 12:22:09
grlloyd authored on 17/09/2019 08:03:04
| ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: structToolbox |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Some tools bult using the struct package |
| 4 |
-Version: 0.4.0 |
|
| 4 |
+Version: 0.7.0 |
|
| 5 | 5 |
Author: Gavin Rhys Lloyd |
| 6 | 6 |
Maintainer: Gavin Rhys Lloyd <[email protected]> |
| 7 | 7 |
Description: Extends the class templates provided by the struct package to provide methods for training PCA, PLS models with cross-validation, permutation testing etc. |
grlloyd authored on 12/09/2019 14:02:34
filters a dataset to only include 'paired' samples i.e. those measured multiple times in different groups e.g. before/after surgery
grlloyd authored on 06/09/2019 13:25:37
grlloyd authored on 25/07/2019 10:18:41
| ... | ... |
@@ -1,7 +1,7 @@ |
| 1 | 1 |
Package: structToolbox |
| 2 | 2 |
Type: Package |
| 3 | 3 |
Title: Some tools bult using the struct package |
| 4 |
-Version: 0.1.0 |
|
| 4 |
+Version: 0.4.0 |
|
| 5 | 5 |
Author: Gavin Rhys Lloyd |
| 6 | 6 |
Maintainer: Gavin Rhys Lloyd <[email protected]> |
| 7 | 7 |
Description: Extends the class templates provided by the struct package to provide methods for training PCA, PLS models with cross-validation, permutation testing etc. |
grlloyd authored on 16/07/2019 08:58:01
grlloyd authored on 12/07/2019 11:56:24
grlloyd authored on 09/07/2019 16:19:29
| ... | ... |
@@ -9,57 +9,58 @@ License: GPL-3 |
| 9 | 9 |
Encoding: UTF-8 |
| 10 | 10 |
LazyData: true |
| 11 | 11 |
Collate: |
| 12 |
- 'anova_class.R' |
|
| 13 |
- 'HSD_class.R' |
|
| 14 |
- 'mixed_effect_class.R' |
|
| 15 |
- 'HSDEM_class.R' |
|
| 16 |
- 'PCA_class.R' |
|
| 17 |
- 'PCA_plotfcns.R' |
|
| 18 |
- 'PLSDA_class.R' |
|
| 19 |
- 'PLSDA_charts.R' |
|
| 20 |
- 'fold_change_class.R' |
|
| 21 |
- 'PLSFC_class.R' |
|
| 22 |
- 'PLSR_class.R' |
|
| 23 |
- 'autoscale_class.R' |
|
| 24 |
- 'balanced_accuracy_class.R' |
|
| 25 |
- 'blank_filter_class.R' |
|
| 26 |
- 'classical_lsq_class.R' |
|
| 27 |
- 'confounders_clsq_class.R' |
|
| 28 |
- 'd_ratio_filter_class.R' |
|
| 29 |
- 'dataset_chart_classes.R' |
|
| 30 |
- 'factor_barchart_class.R' |
|
| 31 |
- 'filter_by_name_class.R' |
|
| 32 |
- 'filter_na_count.R' |
|
| 33 |
- 'filter_smeta_class.R' |
|
| 34 |
- 'fisher_exact_class.R' |
|
| 35 |
- 'fold_change_int_class.R' |
|
| 36 |
- 'forward_selection_by_rank_class.R' |
|
| 37 |
- 'ggplot_theme_pub.R' |
|
| 38 |
- 'glog_class.R' |
|
| 39 |
- 'grid_search_1d_class.R' |
|
| 40 |
- 'hca_class.R' |
|
| 41 |
- 'kfold_xval_class.R' |
|
| 42 |
- 'kfold_xval_charts.R' |
|
| 43 |
- 'knn_impute_class.R' |
|
| 44 |
- 'kw_rank_sum_class.R' |
|
| 45 |
- 'linear_model_class.R' |
|
| 46 |
- 'log_transform.R' |
|
| 47 |
- 'mean_centre_class.R' |
|
| 48 |
- 'mv_feature_filter_class.R' |
|
| 49 |
- 'mv_sample_filter_class.R' |
|
| 50 |
- 'permutation_test_class.R' |
|
| 51 |
- 'permute_sample_order_class.R' |
|
| 52 |
- 'pqn_norm_method_class.R' |
|
| 53 |
- 'prop_na_class.R' |
|
| 54 |
- 'r_squared_class.R' |
|
| 55 |
- 'rsd_filter.R' |
|
| 56 |
- 'sbcms_dataset_class.R' |
|
| 57 |
- 'split_data_class.R' |
|
| 58 |
- 'structToolbox.R' |
|
| 59 |
- 'tSNE_class.R' |
|
| 60 |
- 'ttest_class.R' |
|
| 61 |
- 'vec_norm_class.R' |
|
| 62 |
- 'wilcox_test_class.R' |
|
| 12 |
+ 'anova_class.R' |
|
| 13 |
+ 'HSD_class.R' |
|
| 14 |
+ 'mixed_effect_class.R' |
|
| 15 |
+ 'HSDEM_class.R' |
|
| 16 |
+ 'PCA_class.R' |
|
| 17 |
+ 'PCA_plotfcns.R' |
|
| 18 |
+ 'PLSDA_class.R' |
|
| 19 |
+ 'PLSDA_charts.R' |
|
| 20 |
+ 'fold_change_class.R' |
|
| 21 |
+ 'PLSFC_class.R' |
|
| 22 |
+ 'PLSR_class.R' |
|
| 23 |
+ 'autoscale_class.R' |
|
| 24 |
+ 'balanced_accuracy_class.R' |
|
| 25 |
+ 'blank_filter_class.R' |
|
| 26 |
+ 'classical_lsq_class.R' |
|
| 27 |
+ 'confounders_clsq_class.R' |
|
| 28 |
+ 'd_ratio_filter_class.R' |
|
| 29 |
+ 'dataset_chart_classes.R' |
|
| 30 |
+ 'factor_barchart_class.R' |
|
| 31 |
+ 'feature_profile_class.R' |
|
| 32 |
+ 'filter_by_name_class.R' |
|
| 33 |
+ 'filter_na_count.R' |
|
| 34 |
+ 'filter_smeta_class.R' |
|
| 35 |
+ 'fisher_exact_class.R' |
|
| 36 |
+ 'fold_change_int_class.R' |
|
| 37 |
+ 'forward_selection_by_rank_class.R' |
|
| 38 |
+ 'ggplot_theme_pub.R' |
|
| 39 |
+ 'glog_class.R' |
|
| 40 |
+ 'grid_search_1d_class.R' |
|
| 41 |
+ 'hca_class.R' |
|
| 42 |
+ 'kfold_xval_class.R' |
|
| 43 |
+ 'kfold_xval_charts.R' |
|
| 44 |
+ 'knn_impute_class.R' |
|
| 45 |
+ 'kw_rank_sum_class.R' |
|
| 46 |
+ 'linear_model_class.R' |
|
| 47 |
+ 'log_transform.R' |
|
| 48 |
+ 'mean_centre_class.R' |
|
| 49 |
+ 'mv_feature_filter_class.R' |
|
| 50 |
+ 'mv_sample_filter_class.R' |
|
| 51 |
+ 'permutation_test_class.R' |
|
| 52 |
+ 'permute_sample_order_class.R' |
|
| 53 |
+ 'pqn_norm_method_class.R' |
|
| 54 |
+ 'prop_na_class.R' |
|
| 55 |
+ 'r_squared_class.R' |
|
| 56 |
+ 'rsd_filter.R' |
|
| 57 |
+ 'sbcms_dataset_class.R' |
|
| 58 |
+ 'split_data_class.R' |
|
| 59 |
+ 'structToolbox.R' |
|
| 60 |
+ 'tSNE_class.R' |
|
| 61 |
+ 'ttest_class.R' |
|
| 62 |
+ 'vec_norm_class.R' |
|
| 63 |
+ 'wilcox_test_class.R' |
|
| 63 | 64 |
Depends: struct |
| 64 | 65 |
Imports: ggplot2, |
| 65 | 66 |
pmp, |
grlloyd authored on 09/07/2019 10:44:02
| ... | ... |
@@ -9,81 +9,81 @@ License: GPL-3 |
| 9 | 9 |
Encoding: UTF-8 |
| 10 | 10 |
LazyData: true |
| 11 | 11 |
Collate: |
| 12 |
- 'anova_class.R' |
|
| 13 |
- 'HSD_class.R' |
|
| 14 |
- 'mixed_effect_class.R' |
|
| 15 |
- 'HSDEM_class.R' |
|
| 16 |
- 'PCA_class.R' |
|
| 17 |
- 'PCA_plotfcns.R' |
|
| 18 |
- 'PLSDA_class.R' |
|
| 19 |
- 'PLSDA_charts.R' |
|
| 20 |
- 'fold_change_class.R' |
|
| 21 |
- 'PLSFC_class.R' |
|
| 22 |
- 'PLSR_class.R' |
|
| 23 |
- 'autoscale_class.R' |
|
| 24 |
- 'balanced_accuracy_class.R' |
|
| 25 |
- 'blank_filter_class.R' |
|
| 26 |
- 'classical_lsq_class.R' |
|
| 27 |
- 'confounders_clsq_class.R' |
|
| 28 |
- 'd_ratio_filter_class.R' |
|
| 29 |
- 'dataset_chart_classes.R' |
|
| 30 |
- 'factor_barchart_class.R' |
|
| 31 |
- 'filter_by_name_class.R' |
|
| 32 |
- 'filter_na_count.R' |
|
| 33 |
- 'filter_smeta_class.R' |
|
| 34 |
- 'fisher_exact_class.R' |
|
| 35 |
- 'fold_change_int_class.R' |
|
| 36 |
- 'forward_selection_by_rank_class.R' |
|
| 37 |
- 'ggplot_theme_pub.R' |
|
| 38 |
- 'glog_class.R' |
|
| 39 |
- 'grid_search_1d_class.R' |
|
| 40 |
- 'hca_class.R' |
|
| 41 |
- 'kfold_xval_class.R' |
|
| 42 |
- 'kfold_xval_charts.R' |
|
| 43 |
- 'knn_impute_class.R' |
|
| 44 |
- 'kw_rank_sum_class.R' |
|
| 45 |
- 'linear_model_class.R' |
|
| 46 |
- 'log_transform.R' |
|
| 47 |
- 'mean_centre_class.R' |
|
| 48 |
- 'mv_feature_filter_class.R' |
|
| 49 |
- 'mv_sample_filter_class.R' |
|
| 50 |
- 'permutation_test_class.R' |
|
| 51 |
- 'permute_sample_order_class.R' |
|
| 52 |
- 'pqn_norm_method_class.R' |
|
| 53 |
- 'prop_na_class.R' |
|
| 54 |
- 'r_squared_class.R' |
|
| 55 |
- 'rsd_filter.R' |
|
| 56 |
- 'sbcms_dataset_class.R' |
|
| 57 |
- 'split_data_class.R' |
|
| 58 |
- 'structToolbox.R' |
|
| 59 |
- 'tSNE_class.R' |
|
| 60 |
- 'ttest_class.R' |
|
| 61 |
- 'vec_norm_class.R' |
|
| 62 |
- 'wilcox_test_class.R' |
|
| 12 |
+ 'anova_class.R' |
|
| 13 |
+ 'HSD_class.R' |
|
| 14 |
+ 'mixed_effect_class.R' |
|
| 15 |
+ 'HSDEM_class.R' |
|
| 16 |
+ 'PCA_class.R' |
|
| 17 |
+ 'PCA_plotfcns.R' |
|
| 18 |
+ 'PLSDA_class.R' |
|
| 19 |
+ 'PLSDA_charts.R' |
|
| 20 |
+ 'fold_change_class.R' |
|
| 21 |
+ 'PLSFC_class.R' |
|
| 22 |
+ 'PLSR_class.R' |
|
| 23 |
+ 'autoscale_class.R' |
|
| 24 |
+ 'balanced_accuracy_class.R' |
|
| 25 |
+ 'blank_filter_class.R' |
|
| 26 |
+ 'classical_lsq_class.R' |
|
| 27 |
+ 'confounders_clsq_class.R' |
|
| 28 |
+ 'd_ratio_filter_class.R' |
|
| 29 |
+ 'dataset_chart_classes.R' |
|
| 30 |
+ 'factor_barchart_class.R' |
|
| 31 |
+ 'filter_by_name_class.R' |
|
| 32 |
+ 'filter_na_count.R' |
|
| 33 |
+ 'filter_smeta_class.R' |
|
| 34 |
+ 'fisher_exact_class.R' |
|
| 35 |
+ 'fold_change_int_class.R' |
|
| 36 |
+ 'forward_selection_by_rank_class.R' |
|
| 37 |
+ 'ggplot_theme_pub.R' |
|
| 38 |
+ 'glog_class.R' |
|
| 39 |
+ 'grid_search_1d_class.R' |
|
| 40 |
+ 'hca_class.R' |
|
| 41 |
+ 'kfold_xval_class.R' |
|
| 42 |
+ 'kfold_xval_charts.R' |
|
| 43 |
+ 'knn_impute_class.R' |
|
| 44 |
+ 'kw_rank_sum_class.R' |
|
| 45 |
+ 'linear_model_class.R' |
|
| 46 |
+ 'log_transform.R' |
|
| 47 |
+ 'mean_centre_class.R' |
|
| 48 |
+ 'mv_feature_filter_class.R' |
|
| 49 |
+ 'mv_sample_filter_class.R' |
|
| 50 |
+ 'permutation_test_class.R' |
|
| 51 |
+ 'permute_sample_order_class.R' |
|
| 52 |
+ 'pqn_norm_method_class.R' |
|
| 53 |
+ 'prop_na_class.R' |
|
| 54 |
+ 'r_squared_class.R' |
|
| 55 |
+ 'rsd_filter.R' |
|
| 56 |
+ 'sbcms_dataset_class.R' |
|
| 57 |
+ 'split_data_class.R' |
|
| 58 |
+ 'structToolbox.R' |
|
| 59 |
+ 'tSNE_class.R' |
|
| 60 |
+ 'ttest_class.R' |
|
| 61 |
+ 'vec_norm_class.R' |
|
| 62 |
+ 'wilcox_test_class.R' |
|
| 63 | 63 |
Depends: struct |
| 64 | 64 |
Imports: ggplot2, |
| 65 |
- pmp, |
|
| 66 |
- gridExtra, |
|
| 67 |
- pls, |
|
| 68 |
- sp, |
|
| 69 |
- scales, |
|
| 70 |
- stats, |
|
| 71 |
- methods, |
|
| 72 |
- car, |
|
| 73 |
- grid, |
|
| 74 |
- reshape2, |
|
| 75 |
- agricolae, |
|
| 76 |
- emmeans, |
|
| 77 |
- nlme, |
|
| 78 |
- ggthemes, |
|
| 79 |
- ggdendro, |
|
| 80 |
- Rtsne |
|
| 65 |
+ pmp, |
|
| 66 |
+ gridExtra, |
|
| 67 |
+ pls, |
|
| 68 |
+ sp, |
|
| 69 |
+ scales, |
|
| 70 |
+ stats, |
|
| 71 |
+ methods, |
|
| 72 |
+ car, |
|
| 73 |
+ grid, |
|
| 74 |
+ reshape2, |
|
| 75 |
+ agricolae, |
|
| 76 |
+ emmeans, |
|
| 77 |
+ nlme, |
|
| 78 |
+ ggthemes, |
|
| 79 |
+ ggdendro, |
|
| 80 |
+ Rtsne |
|
| 81 | 81 |
RoxygenNote: 6.1.1 |
| 82 | 82 |
Suggests: |
| 83 |
- testthat, |
|
| 84 |
- covr, |
|
| 85 |
- knitr, |
|
| 86 |
- rmarkdown |
|
| 83 |
+ testthat, |
|
| 84 |
+ covr, |
|
| 85 |
+ knitr, |
|
| 86 |
+ rmarkdown |
|
| 87 | 87 |
Remotes: computational-metabolomics/pmp, |
| 88 | 88 |
computational-metabolomics/struct |
| 89 | 89 |
VignetteBuilder: knitr |
grlloyd authored on 09/07/2019 07:54:00
grlloyd authored on 08/07/2019 14:36:44
| ... | ... |
@@ -40,6 +40,7 @@ Collate: |
| 40 | 40 |
'kfold_xval_class.R' |
| 41 | 41 |
'kfold_xval_charts.R' |
| 42 | 42 |
'knn_impute_class.R' |
| 43 |
+ 'kw_rank_sum_class.R' |
|
| 43 | 44 |
'linear_model_class.R' |
| 44 | 45 |
'log_transform.R' |
| 45 | 46 |
'mean_centre_class.R' |
| ... | ... |
@@ -57,6 +58,7 @@ Collate: |
| 57 | 58 |
'tSNE_class.R' |
| 58 | 59 |
'ttest_class.R' |
| 59 | 60 |
'vec_norm_class.R' |
| 61 |
+ 'wilcox_test_class.R' |
|
| 60 | 62 |
Depends: struct |
| 61 | 63 |
Imports: ggplot2, |
| 62 | 64 |
pmp, |
so that we can use a fcn to load it like we do for iris dataset
grlloyd authored on 08/07/2019 10:54:07
grlloyd authored on 25/06/2019 15:41:56
grlloyd authored on 25/06/2019 15:40:06
grlloyd authored on 14/06/2019 14:05:52
grlloyd authored on 14/06/2019 08:43:03
fold_change for interactions between factors
grlloyd authored on 13/06/2019 13:51:00
grlloyd authored on 04/06/2019 12:24:36
grlloyd authored on 29/05/2019 14:10:02
grlloyd authored on 29/05/2019 13:11:16
| ... | ... |
@@ -67,12 +67,15 @@ Imports: ggplot2, |
| 67 | 67 |
reshape2, |
| 68 | 68 |
agricolae, |
| 69 | 69 |
emmeans, |
| 70 |
- lme4, |
|
| 71 | 70 |
nlme, |
| 72 | 71 |
ggthemes |
| 73 | 72 |
RoxygenNote: 6.1.1 |
| 74 | 73 |
Suggests: |
| 75 | 74 |
testthat, |
| 76 |
- covr |
|
| 75 |
+ covr, |
|
| 76 |
+ knitr, |
|
| 77 |
+ rmarkdown |
|
| 77 | 78 |
Remotes: computational-metabolomics/pmp, |
| 78 | 79 |
computational-metabolomics/struct |
| 80 |
+VignetteBuilder: knitr |
|
| 81 |
+biocViews: WorkflowStep |
Gavin Rhys Lloyd authored on 22/05/2019 09:30:00
• GitHub committed on 22/05/2019 09:30:00
add ci (equivalent to mlr for all components) BETA
inherit fold_change class; allows use of existing plot fcns
grlloyd authored on 13/05/2019 15:11:19
| ... | ... |
@@ -17,6 +17,7 @@ Collate: |
| 17 | 17 |
'PCA_plotfcns.R' |
| 18 | 18 |
'PLSDA_class.R' |
| 19 | 19 |
'PLSDA_charts.R' |
| 20 |
+ 'fold_change_class.R' |
|
| 20 | 21 |
'PLSFC_class.R' |
| 21 | 22 |
'PLSR_class.R' |
| 22 | 23 |
'autoscale_class.R' |
| ... | ... |
@@ -30,7 +31,6 @@ Collate: |
| 30 | 31 |
'filter_na_count.R' |
| 31 | 32 |
'filter_smeta_class.R' |
| 32 | 33 |
'fisher_exact_class.R' |
| 33 |
- 'fold_change_class.R' |
|
| 34 | 34 |
'forward_selection_by_rank_class.R' |
| 35 | 35 |
'ggplot_theme_pub.R' |
| 36 | 36 |
'glog_class.R' |
(experimental) use PLS model inversion to calculate fold change
grlloyd authored on 10/05/2019 14:20:57
incomplete and non-functional. may be added again at another time depending on requirements.
grlloyd authored on 09/04/2019 14:35:49
grlloyd authored on 02/04/2019 16:26:09
| ... | ... |
@@ -31,6 +31,7 @@ Collate: |
| 31 | 31 |
'filter_smeta_class.R' |
| 32 | 32 |
'fisher_exact_class.R' |
| 33 | 33 |
'forward_selection_by_rank_class.R' |
| 34 |
+ 'ggplot_theme_pub.R' |
|
| 34 | 35 |
'glog_class.R' |
| 35 | 36 |
'grid_search_1d_class.R' |
| 36 | 37 |
'kfold_xval_class.R' |
| ... | ... |
@@ -66,7 +67,8 @@ Imports: ggplot2, |
| 66 | 67 |
agricolae, |
| 67 | 68 |
emmeans, |
| 68 | 69 |
lme4, |
| 69 |
- nlme |
|
| 70 |
+ nlme, |
|
| 71 |
+ ggthemes |
|
| 70 | 72 |
RoxygenNote: 6.1.1 |
| 71 | 73 |
Suggests: |
| 72 | 74 |
testthat, |
struct now searches for parameters labelled param. and output. so list of them no longer needed as a slot
grlloyd authored on 01/04/2019 14:10:06
grlloyd authored on 01/04/2019 12:27:13
grlloyd authored on 01/04/2019 12:23:12
grlloyd authored on 01/04/2019 10:31:02
for struct and pmp while in development
grlloyd authored on 01/04/2019 10:21:32
| ... | ... |
@@ -11,6 +11,8 @@ LazyData: true |
| 11 | 11 |
Collate: |
| 12 | 12 |
'anova_class.R' |
| 13 | 13 |
'HSD_class.R' |
| 14 |
+ 'mixed_effect_class.R' |
|
| 15 |
+ 'HSDEM_class.R' |
|
| 14 | 16 |
'PCA_class.R' |
| 15 | 17 |
'PCA_plotfcns.R' |
| 16 | 18 |
'PLSDA_class.R' |
| ... | ... |
@@ -37,7 +39,6 @@ Collate: |
| 37 | 39 |
'linear_model_class.R' |
| 38 | 40 |
'log_transform.R' |
| 39 | 41 |
'mean_centre_class.R' |
| 40 |
- 'mixed_effect_class.R' |
|
| 41 | 42 |
'mv_feature_filter_class.R' |
| 42 | 43 |
'mv_sample_filter_class.R' |
| 43 | 44 |
'permutation_test_class.R' |
| ... | ... |
@@ -66,5 +67,5 @@ Imports: ggplot2, |
| 66 | 67 |
reshape2, |
| 67 | 68 |
agricolae, |
| 68 | 69 |
emmeans, |
| 69 |
- lmerTest |
|
| 70 |
+ lme4 |
|
| 70 | 71 |
RoxygenNote: 6.1.1 |
Gavin Rhys Lloyd authored on 20/03/2019 15:54:08
| 1 | 1 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,70 @@ |
| 1 |
+Package: structtoolbox |
|
| 2 |
+Type: Package |
|
| 3 |
+Title: Some tools bult using the struct package |
|
| 4 |
+Version: 0.1.0 |
|
| 5 |
+Author: Gavin Rhys Lloyd |
|
| 6 |
+Maintainer: Gavin Rhys Lloyd <[email protected]> |
|
| 7 |
+Description: Extends the class templates provided by the struct package to provide methods for training PCA, PLS models with cross-validation, permutation testing etc. |
|
| 8 |
+License: GPL-3 |
|
| 9 |
+Encoding: UTF-8 |
|
| 10 |
+LazyData: true |
|
| 11 |
+Collate: |
|
| 12 |
+ 'anova_class.R' |
|
| 13 |
+ 'HSD_class.R' |
|
| 14 |
+ 'PCA_class.R' |
|
| 15 |
+ 'PCA_plotfcns.R' |
|
| 16 |
+ 'PLSDA_class.R' |
|
| 17 |
+ 'PLSDA_charts.R' |
|
| 18 |
+ 'PLSR_class.R' |
|
| 19 |
+ 'autoscale_class.R' |
|
| 20 |
+ 'balanced_accuracy_class.R' |
|
| 21 |
+ 'blank_filter_class.R' |
|
| 22 |
+ 'classical_lsq_class.R' |
|
| 23 |
+ 'confounders_clsq_class.R' |
|
| 24 |
+ 'dataset_chart_classes.R' |
|
| 25 |
+ 'factor_barchart_class.R' |
|
| 26 |
+ 'filter_by_name_class.R' |
|
| 27 |
+ 'filter_na_count.R' |
|
| 28 |
+ 'filter_pca_outliers_class.R' |
|
| 29 |
+ 'filter_smeta_class.R' |
|
| 30 |
+ 'fisher_exact_class.R' |
|
| 31 |
+ 'forward_selection_by_rank_class.R' |
|
| 32 |
+ 'glog_class.R' |
|
| 33 |
+ 'grid_search_1d_class.R' |
|
| 34 |
+ 'kfold_xval_class.R' |
|
| 35 |
+ 'kfold_xval_charts.R' |
|
| 36 |
+ 'knn_impute_class.R' |
|
| 37 |
+ 'linear_model_class.R' |
|
| 38 |
+ 'log_transform.R' |
|
| 39 |
+ 'mean_centre_class.R' |
|
| 40 |
+ 'mixed_effect_class.R' |
|
| 41 |
+ 'mv_feature_filter_class.R' |
|
| 42 |
+ 'mv_sample_filter_class.R' |
|
| 43 |
+ 'permutation_test_class.R' |
|
| 44 |
+ 'permute_sample_order_class.R' |
|
| 45 |
+ 'pqn_norm_method_class.R' |
|
| 46 |
+ 'prop_na_class.R' |
|
| 47 |
+ 'r_squared_class.R' |
|
| 48 |
+ 'rsd_filter.R' |
|
| 49 |
+ 'split_data_class.R' |
|
| 50 |
+ 'structtoolbox.R' |
|
| 51 |
+ 'ttest_class.R' |
|
| 52 |
+ 'ttest_plotfcns.R' |
|
| 53 |
+ 'univarate_ancova.R' |
|
| 54 |
+ 'vec_norm_class.R' |
|
| 55 |
+Depends: struct |
|
| 56 |
+Imports: ggplot2, |
|
| 57 |
+ pmp, |
|
| 58 |
+ gridExtra, |
|
| 59 |
+ pls, |
|
| 60 |
+ sp, |
|
| 61 |
+ scales, |
|
| 62 |
+ stats, |
|
| 63 |
+ methods, |
|
| 64 |
+ car, |
|
| 65 |
+ grid, |
|
| 66 |
+ reshape2, |
|
| 67 |
+ agricolae, |
|
| 68 |
+ emmeans, |
|
| 69 |
+ lmerTest |
|
| 70 |
+RoxygenNote: 6.1.1 |