From ef7dffbed2f77c2854c2b02411a01866fb4795f6 Mon Sep 17 00:00:00 2001 From: Maximilian Koehler <91941870+MrMaximumMax@users.noreply.github.com> Date: Thu, 17 Mar 2022 14:18:19 +0100 Subject: [PATCH] Update files via upload --- man/add_clust2enrich.Rd | 2 +- man/add_clust2ts.Rd | 2 +- man/add_enrich.Rd | 2 +- man/clValid_flow.Rd | 2 +- man/clust_matrix.Rd | 2 +- man/emd_heatmap.Rd | 2 +- man/emd_matrix.Rd | 2 +- man/enr_obs_clust.Rd | 2 +- man/jaccard_run_cognate.Rd | 2 +- man/max_fluc.Rd | 2 +- man/patient_boxplot.Rd | 2 +- man/patient_hist.Rd | 2 +- man/patient_list.Rd | 2 +- man/patient_ts_plot.Rd | 2 +- man/rnd_dat_rm.Rd | 2 +- man/sim_jaccard_cognate.Rd | 2 +- man/sim_jaccard_emd.Rd | 2 +- man/sim_sample_enr.Rd | 2 +- 18 files changed, 18 insertions(+), 18 deletions(-) diff --git a/man/add_clust2enrich.Rd b/man/add_clust2enrich.Rd index ff51528..908451c 100644 --- a/man/add_clust2enrich.Rd +++ b/man/add_clust2enrich.Rd @@ -19,7 +19,7 @@ Add clustering assignments to enrichment data frame } \examples{ list <- patient_list('.../ts_demofiles1') #Just folder; files can be pulled from GitHub demo files -(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) +#(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) #Sampling frequency is supposed to be daily clustering <- clust_matrix(matrix, method = "kmeans", nclust = 3) enr <- add_enrich(list, '.../enrichment_dat.csv') #file can be pulled from GitHub demo files diff --git a/man/add_clust2ts.Rd b/man/add_clust2ts.Rd index 060432e..78fb7fd 100644 --- a/man/add_clust2ts.Rd +++ b/man/add_clust2ts.Rd @@ -19,7 +19,7 @@ Add clustering assignments to time series data } \examples{ list <- patient_list('.../ts_demofiles1') #Just folder; files can be pulled from GitHub demo files -(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) +#(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) #Sampling frequency is supposed to be daily clustering <- clust_matrix(matrix, method = "kmeans", nclust = 3) ts <- add_clust2ts(list, clustering) diff --git a/man/add_enrich.Rd b/man/add_enrich.Rd index 4b32f6f..9f325ca 100644 --- a/man/add_enrich.Rd +++ b/man/add_enrich.Rd @@ -19,7 +19,7 @@ Add enrichment data and preprocess for analysis } \examples{ list <- patient_list('.../ts_demofiles1') #Just folder; files can be pulled from GitHub demo files -(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) +#(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) #Sampling frequency is supposed to be daily enr <- add_enrich(list, '.../enrichment_dat.csv') #file can be pulled from GitHub demo files } diff --git a/man/clValid_flow.Rd b/man/clValid_flow.Rd index ab8d6bc..67da24f 100644 --- a/man/clValid_flow.Rd +++ b/man/clValid_flow.Rd @@ -19,7 +19,7 @@ Interactive console workflow to calculate and evaluate cluster validation measur } \examples{ list <- patient_list('.../ts_demofiles2') #file can be pulled from GitHub demo files -(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles2) +#(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles2) #Sampling frequency is twice daily distmat <- emd_matrix(list, "PEF", maxIter = 5000) parameters <- init_clValid() diff --git a/man/clust_matrix.Rd b/man/clust_matrix.Rd index 6361d4f..6ee68b8 100644 --- a/man/clust_matrix.Rd +++ b/man/clust_matrix.Rd @@ -23,7 +23,7 @@ Cluster Earth Mover Distance Square Matrix data } \examples{ list <- patient_list('.../ts_demofiles1') #Just folder; files can be pulled from GitHub demo files -(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) +#(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) #Sampling frequency is supposed to be daily matrix <- emd_matrix(list, "FEV1") clustering <- clust_matrix(matrix, method = "hierarchical", nclust = 2) diff --git a/man/emd_heatmap.Rd b/man/emd_heatmap.Rd index 211ea8e..5e88ff4 100644 --- a/man/emd_heatmap.Rd +++ b/man/emd_heatmap.Rd @@ -19,7 +19,7 @@ Visualize an Earth Mover's Distance Square Matrix as a heatmap } \examples{ list <- patient_list('.../ts_demofiles1') #Just folder; files can be pulled from GitHub demo files -(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) +#(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) #Sampling frequency is supposed to be daily matrix <- emd_matrix(list, "FEV1") emd_heatmap(matrix) diff --git a/man/emd_matrix.Rd b/man/emd_matrix.Rd index c19843e..851326e 100644 --- a/man/emd_matrix.Rd +++ b/man/emd_matrix.Rd @@ -21,7 +21,7 @@ Generate a Earth Mover's Distance Matrix out of time series data list entries } \examples{ list <- patient_list('.../ts_demofiles1') #Just folder; files can be pulled from GitHub demo files -(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) +#(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) #Sampling frequency is supposed to be daily matrix <- emd_matrix(list, "FEV1") } diff --git a/man/enr_obs_clust.Rd b/man/enr_obs_clust.Rd index 94ce8d3..d5a2735 100644 --- a/man/enr_obs_clust.Rd +++ b/man/enr_obs_clust.Rd @@ -21,7 +21,7 @@ Observe specific cluster for overview and p-values } \examples{ list <- patient_list('.../ts_demofiles1') #Just folder; files can be pulled from GitHub demo files -(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) +#(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) #Sampling frequency is supposed to be daily clustering <- clust_matrix(matrix, method = "kmeans", nclust = 3) enr <- add_enrich(list, '.../enrichment_dat.csv') #file can be drawn from GitHub demo files diff --git a/man/jaccard_run_cognate.Rd b/man/jaccard_run_cognate.Rd index 5d08f3f..d07b53d 100644 --- a/man/jaccard_run_cognate.Rd +++ b/man/jaccard_run_cognate.Rd @@ -37,7 +37,7 @@ Simulate random data removal from time series data list and determine Jaccard in } \examples{ list <- patient_list('.../ts_demofiles1') #Just folder; files can be pulled from GitHub demo files -(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) +#(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) #Sampling frequency is supposed to be daily output <- jaccard_run_cognate(list,"PEF",10,"hierarchical",1,3,c(0.005,0.01,0.05,0.1,0.2)) } diff --git a/man/max_fluc.Rd b/man/max_fluc.Rd index fccc24d..71f4503 100644 --- a/man/max_fluc.Rd +++ b/man/max_fluc.Rd @@ -19,7 +19,7 @@ Determine pair of maximum fluctuation difference in a list storing time series d } \examples{ list <- patient_list('.../ts_demofiles1') #Just folder; files can be pulled from GitHub demo files -(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) +#(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) #Sampling frequency is supposed to be daily matrix <- emd_matrix(list, "FEV1") max_fluc(list, "PEF") diff --git a/man/patient_boxplot.Rd b/man/patient_boxplot.Rd index 1c9e79f..e84a5c6 100644 --- a/man/patient_boxplot.Rd +++ b/man/patient_boxplot.Rd @@ -23,7 +23,7 @@ Visualize patient(s) time series data in a boxplot for indicated parameter } \examples{ list <- patient_list('.../ts_demofiles1') #Just folder; files can be pulled from GitHub demo files -(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) +#(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) #Sampling frequency is supposed to be daily patient_boxplot(list,c("ID_2","testpat_1","testpat_2","a301"), "FEV1") } diff --git a/man/patient_hist.Rd b/man/patient_hist.Rd index f3ab63a..21ea2a8 100644 --- a/man/patient_hist.Rd +++ b/man/patient_hist.Rd @@ -23,7 +23,7 @@ Visualize patient time series data in a histogram for indicated parameter } \examples{ list <- patient_list('.../ts_demofiles1') #Just folder; files can be pulled from GitHub demo files -(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) +#(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) #Sampling frequency is supposed to be daily patient_hist(list,"testpat_1","PEF") } diff --git a/man/patient_list.Rd b/man/patient_list.Rd index b30e84c..19850fd 100644 --- a/man/patient_list.Rd +++ b/man/patient_list.Rd @@ -17,6 +17,6 @@ Process patient time series data by interpolation options and store data in an o } \examples{ list <- patient_list('.../ts_demofiles1') #files can be pulled from GitHub demo files -(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) +#(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) #Sampling frequency is supposed to be daily } diff --git a/man/patient_ts_plot.Rd b/man/patient_ts_plot.Rd index 94dc9fe..b865dd0 100644 --- a/man/patient_ts_plot.Rd +++ b/man/patient_ts_plot.Rd @@ -23,7 +23,7 @@ Visualize patient time series data in a time series plot for indicated parameter } \examples{ list <- patient_list('.../ts_demofiles1') #Just folder; files can be pulled from GitHub demo files -(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) +#(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) #Sampling frequency is supposed to be daily patient_ts_plot(list,"testpat_1","PEF") } diff --git a/man/rnd_dat_rm.Rd b/man/rnd_dat_rm.Rd index af60ce5..c011b62 100644 --- a/man/rnd_dat_rm.Rd +++ b/man/rnd_dat_rm.Rd @@ -19,7 +19,7 @@ Remove random data from time series data list } \examples{ list <- patient_list('.../ts_demofiles1') #Just folder; files can be pulled from GitHub demo files -(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) +#(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) #Sampling frequency is supposed to be daily list_rm <- rnd_dat_rm(testlist, 0.95) } diff --git a/man/sim_jaccard_cognate.Rd b/man/sim_jaccard_cognate.Rd index 0897b4f..a997a58 100644 --- a/man/sim_jaccard_cognate.Rd +++ b/man/sim_jaccard_cognate.Rd @@ -29,7 +29,7 @@ Simulate random data removal from time series data list and determine Jaccard in } \examples{ list <- patient_list('.../ts_demofiles1') #Just folder; files can be pulled from GitHub demo files -(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) +#(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) #Sampling frequency is supposed to be daily output <- sim_jaccard_cognate(list, "PEF", 0.05, 10, "hierarchical", 2, 1000) } diff --git a/man/sim_jaccard_emd.Rd b/man/sim_jaccard_emd.Rd index a3815f3..0cb920f 100644 --- a/man/sim_jaccard_emd.Rd +++ b/man/sim_jaccard_emd.Rd @@ -29,7 +29,7 @@ Simulate random data removal from time series data list and determine Jaccard in } \examples{ list <- patient_list('.../ts_demofiles1') #Just folder; files can be pulled from GitHub demo files -(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) +#(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) #Sampling frequency is supposed to be daily output <- sim_jaccard_emd(list, "PEF", 0.05, 10, "hierarchical", 2, 1000) } diff --git a/man/sim_sample_enr.Rd b/man/sim_sample_enr.Rd index 6f61b56..8061e31 100644 --- a/man/sim_sample_enr.Rd +++ b/man/sim_sample_enr.Rd @@ -25,7 +25,7 @@ Simulate random sampling for NA entries in enrichment data and check stability o } \examples{ list <- patient_list('.../ts_demofiles1') #Just folder; files can be pulled from GitHub demo files -(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) +#(https://github.com/MrMaximumMax/FBCanalysis/tree/master/demo_and_testfiles/ts_demofiles1) #Sampling frequency is supposed to be daily test <- sim_sample_enr(list,path,clustering,1,100) sim_sample_enr <- function(plist, path, clustdat, clustno, n_sim)