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• 49b7f0e564 added TO_DO in mosaic from panino master Tanushree Tunstall 2023-04-27 14:06:41 +01:00
• 2f7090139e just added minor checks for numbers and stats Tanushree Tunstall 2022-11-19 16:46:34 +00:00
• 7011dc75fa added boxplots_stat_ob_paper.R and plot_data_ob_paper.R Tanushree Tunstall 2022-11-18 17:20:07 +00:00
• dc7e277a72 updated boxplot_stat_function to now take custom order of mediators to plot Tanushree Tunstall 2022-11-18 17:19:06 +00:00
• 1f9e5f4e8c minor change in read_data.R to uncomment metadata_all which is required for downstream processing Tanushree Tunstall 2022-11-17 17:52:51 +00:00
• 28a356fc19 added unpaired stats for asthma and severe for sam, serum and npa Tanushree Tunstall 2020-12-08 13:00:17 +00:00
• 9acc36c8de saving work Tanushree Tunstall 2020-12-08 12:56:28 +00:00
• 74c4dd878c adde asthma and severity analysis dir Tanushree Tunstall 2020-12-08 04:04:11 +00:00
• 3338de800a added and moved plot_data for non-asthmatics and non-severe analysis Tanushree Tunstall 2020-12-07 16:55:17 +00:00
• c3b1ba9a0e added boxplots with stats for non-severe analysis Tanushree Tunstall 2020-12-07 16:52:34 +00:00
• dde2cc9494 checked and tidy up scripts for plots for non-severe Tanushree Tunstall 2020-12-07 16:51:16 +00:00
• f2b778ace7 moved non-asthmatics analysis to non_asthmatics/ Tanushree Tunstall 2020-11-30 12:15:11 +00:00
• 6731b9484c added check_stats.R for non-severe analysis Tanushree Tunstall 2020-11-30 12:06:55 +00:00
• 37f8cd619e added stats for non_severe flu stats in resp dir Tanushree Tunstall 2020-11-27 18:22:00 +00:00
• 47a03c2639 saving work Tanushree Tunstall 2020-11-27 18:21:35 +00:00
• a43f323ed8 reflected new filename in source scripts! Tanushree Tunstall 2020-11-27 17:53:40 +00:00
• 3a380a5be1 renamed file to reflect data_extraction_mediator Tanushree Tunstall 2020-11-27 17:47:05 +00:00
• 52a2453327 saving work Tanushree Tunstall 2020-11-24 18:53:02 +00:00
• f0c0fd72d1 perfomed LR analysis and tidyed up clinical formatting code Tanushree Tunstall 2020-11-24 18:46:47 +00:00
• 08e01abfb5 correcting dtype for sfluv and h1n1v for data formatting clinical Tanushree Tunstall 2020-11-24 13:48:53 +00:00
• 7529549bfc added obesity and asthma as covariates with t1_resp score as outcome Tanushree Tunstall 2020-11-23 18:31:19 +00:00
• 9158866dda added regression for meds with death outcome Tanushree Tunstall 2020-11-23 18:24:30 +00:00
• 4800f804e4 moved non-asthmatics scripts back Tanushree Tunstall 2020-11-23 18:18:32 +00:00
• a53243a19c moved older regression files to extra Tanushree Tunstall 2020-11-23 18:17:08 +00:00
• e3259f2f17 logistic regression for outcome and meds Tanushree Tunstall 2020-11-23 18:16:19 +00:00
• 25fb702e2e added boxplots for non-asthmatics i.e wq boxplot_linear_na.R boxplot_log_na.R Tanushree Tunstall 2020-11-20 13:16:53 +00:00
• e71a2ccd40 added plot_data_na.R for plotting non-asthmatics fp adults Tanushree Tunstall 2020-11-20 13:15:49 +00:00
• 3b6776af24 saving work Tanushree Tunstall 2020-11-20 13:14:10 +00:00
• 0d591c46f5 added non asthmatics stats for sam and serum flu_stats_unpaired_na_sam.R and flu_stats_unpaired_na_serum.R Tanushree Tunstall 2020-11-20 12:38:10 +00:00
• 1562a09631 added quick summary to see sig meds just before writing file Tanushree Tunstall 2020-11-20 12:36:55 +00:00
• 17aebc26e8 added non asthmatics analysis data_extraction_formatting_non_asthmatics.R and flu_stats_unpaired_na_npa.R Tanushree Tunstall 2020-11-20 11:43:56 +00:00
• b72c4df796 reformatting code to select needed df for analysis Tanushree Tunstall 2020-11-20 11:43:03 +00:00
• a6cbaab40a added flu_stats_fisher_only.R containing separate dfs based on var factor levels Tanushree Tunstall 2020-11-19 18:05:57 +00:00
• 74769b9a38 cleaninig code Tanushree Tunstall 2020-11-19 18:04:59 +00:00
• 269918d696 separated fisher test only and renamed logistic_outcome col Tanushree Tunstall 2020-11-19 17:48:08 +00:00
• 6e999898df stats for categ vars using chisq and fisher Tanushree Tunstall 2020-11-19 15:40:02 +00:00
• 46575c657f saving Tanushree Tunstall 2020-11-19 15:39:18 +00:00
• c5529206d9 added steroid_ics data for merging with clinical data for completion Tanushree Tunstall 2020-11-18 16:35:10 +00:00
• 702ff4e327 renamed reg_cols_extraction.R to colnames_clinical_meds.R Tanushree Tunstall 2020-11-18 16:11:35 +00:00
• 66f49a0eed added extra/ Tanushree Tunstall 2020-11-18 16:04:30 +00:00
• 76dc3fbb6b added data_extraction_formatting_regression.R flu_stats_unpaired_clinical.R and reg_cols_extraction.R Tanushree Tunstall 2020-11-18 16:01:29 +00:00
• bb6e92fa0f separated clinical data processing from reg Tanushree Tunstall 2020-11-18 16:00:26 +00:00
• 9dbad32504 added checks for fp adults in read_data.R Tanushree Tunstall 2020-11-18 13:08:39 +00:00
• 07de043cab updated read_data.R to return fp_adults as well Tanushree Tunstall 2020-11-18 13:06:36 +00:00
• 12eee6923a added checks.R Tanushree Tunstall 2020-11-17 17:31:22 +00:00
• 4766d6d450 added clinical data extraction and logistic regression script Tanushree Tunstall 2020-11-17 17:30:05 +00:00
• 05f1f716f1 updated Header_TT.R with reg libs Tanushree Tunstall 2020-11-17 17:29:24 +00:00
• ba3c4564ea ran quick stats checks with wf data Tanushree Tunstall 2020-11-02 18:31:29 +00:00
• f14c7ca64b outputting svg for plots with stats Tanushree Tunstall 2020-11-02 17:20:38 +00:00
• b94d9a3fdb renamed file to reflect stats for linear graphs Tanushree Tunstall 2020-11-02 16:39:37 +00:00
• abf615baeb removed boxplot_function as try error handle sit now! Tanushree Tunstall 2020-11-02 16:37:44 +00:00
• a4d305d44b added TASK at the beginning of the scripts Tanushree Tunstall 2020-11-02 16:36:52 +00:00
• 8033c1785f added try catch for error handling Tanushree Tunstall 2020-11-02 16:26:22 +00:00
• 9c141326aa enter the commit message for your changes. Lines starting Tanushree Tunstall 2020-11-02 15:04:40 +00:00
• b8ff7995ac added boxplot_stat_log.R to generate graphs with log data and stats Tanushree Tunstall 2020-11-02 14:28:52 +00:00
• 550e8b2c50 renamed file Tanushree Tunstall 2020-11-02 12:06:46 +00:00
• 9fc9a5852b renamed file Tanushree Tunstall 2020-11-02 12:05:55 +00:00
• ee35e1cb20 renamed file boxplot_stat.R to boxplot_stat_all.R Tanushree Tunstall 2020-11-02 11:37:22 +00:00
• 26f90ee2c0 added plot_data.R to source for plotting Tanushree Tunstall 2020-11-01 16:47:54 +00:00
• 4ca975bf81 added boxplot_stat.R to output plots for all sample types Tanushree Tunstall 2020-11-01 16:46:42 +00:00
• dc775a4486 added boxplot_stat_test.R to test boxplot_stat_function independently Tanushree Tunstall 2020-11-01 16:46:09 +00:00
• c0d993b232 isolating function from running on data Tanushree Tunstall 2020-11-01 16:44:42 +00:00
• eaa8416255 changed cols for groups Tanushree Tunstall 2020-10-31 20:53:44 +00:00
• 6375a53feb rendering formatted pvalue on graph Tanushree Tunstall 2020-10-31 20:46:06 +00:00
• dd54f10ad8 making it work with function and ggarrange to combine plots Tanushree Tunstall 2020-10-31 20:43:07 +00:00
• 6575fc7aba updating the function Tanushree Tunstall 2020-10-31 19:52:18 +00:00
• 9c67a208e2 added annotation to the plot with annotate, still testing Tanushree Tunstall 2020-10-31 19:30:12 +00:00
• 558f57c61e tweaking layout in test Tanushree Tunstall 2020-10-31 18:30:20 +00:00
• 8015dd4d6a fixed colours as well Tanushree Tunstall 2020-10-30 20:56:15 +00:00
• 1ed09ac20b nearly, adding correct y_pos to plot the stat labels Tanushree Tunstall 2020-10-30 19:48:28 +00:00
• af334b559e added boxplot_stat_function.R Tanushree Tunstall 2020-10-30 17:23:40 +00:00
• 3274d3f08b testing boxplot with stats Tanushree Tunstall 2020-10-30 17:22:46 +00:00
• ed10be8f6e testing boxplots Tanushree Tunstall 2020-10-30 17:10:20 +00:00
• 8358c0862c renamed file Tanushree Tunstall 2020-10-30 17:06:27 +00:00
• 9921f92fba saving work Tanushree Tunstall 2020-10-30 13:30:58 +00:00
• ff1de17718 saving work Tanushree Tunstall 2020-10-30 13:24:11 +00:00
• d854f8f750 added log bpxplots i.e boxplot_log.R Tanushree Tunstall 2020-10-30 13:23:29 +00:00
• 7946d8cf72 minor edit to titles Tanushree Tunstall 2020-10-30 13:22:47 +00:00
• d512fd4e34 added boxplot_linear.R to separate linear and log plots Tanushree Tunstall 2020-10-30 13:14:42 +00:00
• 936bc23aa2 added summary_stats_time_group for sam and serum Tanushree Tunstall 2020-10-30 13:06:02 +00:00
• a2dbecd03d updated un[aired stats with n_obs_complete and removed mediator vitd from sam and npa Tanushree Tunstall 2020-10-30 13:04:45 +00:00
• 1b5d353060 added summary_stats_time_group_npa.R for NPA Tanushree Tunstall 2020-10-30 11:57:08 +00:00
• 15bba91cee updated header file with packes for summary stats Tanushree Tunstall 2020-10-30 11:53:26 +00:00
• 7463f9ac1c ploting npa before sam and serum for boxplots Tanushree Tunstall 2020-10-29 18:56:31 +00:00
• 540b6c5bf7 generating plots for all sample types withoout stats Tanushree Tunstall 2020-10-29 18:50:25 +00:00
• c26171d12c playing with display Tanushree Tunstall 2020-10-29 17:41:39 +00:00
• 2634aeeb84 added boxplot.R Tanushree Tunstall 2020-10-29 16:57:27 +00:00
• ad537a3ace added "/" at the end of outdir_plots Tanushree Tunstall 2020-10-29 13:26:09 +00:00
• e1f97df805 ran scripts to check Tanushree Tunstall 2020-10-29 13:20:51 +00:00
• 1e6e9eaef1 tidy scripts and using age as criteria for adults Tanushree Tunstall 2020-10-29 13:10:39 +00:00
• 49c18d390f trychecking if summary stats may be added to the output Tanushree Tunstall 2020-10-29 12:44:35 +00:00
• bbdd2d12e5 changed df to adults df to extract relevant info Tanushree Tunstall 2020-10-29 10:45:49 +00:00
• 9e5b202f5d added legend_adjustment.R and included this in Header_TT Tanushree Tunstall 2020-10-26 21:40:24 +00:00
• a50cb6d331 ah, found it, added lf data number check to flu stats Tanushree Tunstall 2020-10-26 20:18:26 +00:00
• 6da0bd2e00 added stats_check.R to cross check Tanushree Tunstall 2020-10-26 20:16:24 +00:00
• f13d1212e9 apparently modifed flu stats for npa: check! Tanushree Tunstall 2020-10-26 20:15:44 +00:00
• ae1e663caf name generation for output files for other stats Tanushree Tunstall 2020-10-26 16:18:20 +00:00
• 6e54f339d1 reformatted to generate outfile_name for flu stats Tanushree Tunstall 2020-10-26 16:12:51 +00:00
• 61fbb2f8d6 formatted non-flu stats in the same way as the flu ones Tanushree Tunstall 2020-10-26 14:33:20 +00:00
• efcdb1a34d renamed files Tanushree Tunstall 2020-10-26 13:55:16 +00:00