updated news for survival

sbalci · May 23, 2020 · 301c3e1 · 301c3e1
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diff --git a/NEWS.md b/NEWS.md
@@ -61,6 +61,54 @@ https://www.youtube.com/watch?v=m3uInetiC8w
 https://twitter.com/serdarbalci/status/1263191858454413312
 
 
+- Some examples of survival analysis via @jamovistats #ClinicoPath module.
+Using #rstats #finalfit by @ewenharrison #survival #survminer #ggstatsplot in #jamovi
+#biostatistics #pathology #pathologists 
+https://www.youtube.com/watch?v=gIPf4xIKAOU
+
+https://www.linkedin.com/pulse/survival-analysis-via-jamovi-clinicopath-module-serdar-balc%25C4%25B1 #datavisualisation #datascience #patoloji #analysis #datascientist #data #clinicaltrials #clinicalstudies #clinicaltrial #clinicalresearch 
+
+
+https://twitter.com/serdarbalci/status/1264153665386004480
+
+It is generating natural language summaries to make easy to read the tables:
+"Median Survival:
+When LVI is Absent, median survival is 26 [20.1 - 32.3,”95% CI] months.
+When LVI is Present, median survival is 9.3 [8.8 - 10.6, 95% CI] months."
+
+https://twitter.com/serdarbalci/status/1264153686508478465
+
+“Hazard:
+When LVI is Present, there is 2.55 (1.85-3.51, p<0.001) times risk than when LVI is Absent.”
+
+https://twitter.com/serdarbalci/status/1264153695715053568
+
+"1, 3, 5-yr Survival:
+When LVI Absent, 12 month survival is 70.9% [63.36%-79.3%, 95% CI]. When LVI Absent, 24 month survival is 54.2% [45.85%-64.1%, When LVI Present, 12 month survival is 28.4% [20.03%-40.3%, 95% CI]. When LVI Present, 24 month survival is 14.4% …”
+
+https://twitter.com/serdarbalci/status/1264153698764312577
+
+"pairwise comparison of Grade:
+The comparison between Grade 2 and Grade 1 has a p-value of 0.87."
+Note for myself: The wording should be better.
+
+https://twitter.com/serdarbalci/status/1264153700114862080
+
+You can do multivariate survival analysis
+
+https://twitter.com/serdarbalci/status/1264153711087140864
+
+And also make Odds Ratio Tables and Plots.
+When you change the order of variables in jamovi data, the analysis also changes.
+
+https://twitter.com/serdarbalci/status/1264153752015122432
+
+
+https://github.com/sbalci/ClinicoPathJamoviModule
+
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/videoseries?list=PLxRBOaoEoP4JfAMi7aIbkRXPXGUEwzTNv" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+
 
 
 

diff --git a/README.Rmd b/README.Rmd
@@ -220,6 +220,11 @@ https://osf.io/9szud/
 #### Odds Ratio Table and Plot 
 
 
+<img src="man/figures/jamovi-ClinicoPath-oddsratio.gif" align="center" width = 75% />
+
+
+
+
 
 #### Competing Survival
 
@@ -349,8 +354,9 @@ See https://github.com/ClinicoPath for forked packages.
 
 ---
 
-<a class="twitter-follow-button" data-show-count="false" href="https://twitter.com/serdarbalci">Follow @serdarbalci</a><script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
-<a class="bmc-button" target="_blank" href="https://www.buymeacoffee.com/bS0teIs"><img src="https://cdn.buymeacoffee.com/buttons/bmc-new-btn-logo.svg" alt="Buy me a coffee"><span style="margin-left:15px;font-size:28px !important;">Buy me a coffee</span></a>
+<a class="twitter-follow-button" data-show-count="false" href="https://twitter.com/serdarbalci">Follow @serdarbalci</a><script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>  
+
+<a class="bmc-button" target="_blank" href="https://www.buymeacoffee.com/bS0teIs"><img src="https://cdn.buymeacoffee.com/buttons/bmc-new-btn-logo.svg" alt="Buy me a coffee"><span style="margin-left:15px;font-size:28px !important;">Buy me a coffee</span></a>  
 
 https://paypal.me/serdarbalci
 
@@ -474,3 +480,8 @@ https://paypal.me/serdarbalci
 [![contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg?style=flat)](https://github.com/sbalci/clinicopathjamovimodule/issues)
 ![GitHub watchers](https://img.shields.io/github/watchers/sbalci/clinicopathjamovimodule?style=social)
 
+
+## Videos
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/videoseries?list=PLxRBOaoEoP4JfAMi7aIbkRXPXGUEwzTNv" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>
+
diff --git a/data/histopathologyanalysis.omv b/data/histopathologyanalysis.omv
diff --git a/man/figures/jamovi-ClinicoPath-oddsratio.gif b/man/figures/jamovi-ClinicoPath-oddsratio.gif
diff --git a/tododata/todo.Rmd b/tododata/todo.Rmd
@@ -1007,15 +1007,85 @@ usethis::use_data(histopathology)
 ```
 
 
+## force git
+
+```{r force git, eval=FALSE, include=FALSE}
+# gitUpdateCommitPush
+CommitMessage <- paste("updated on ", Sys.time(), sep = "")
+wd <- getwd()
+gitCommand <- paste("cd ", wd, " \n git add . \n git commit --message '", CommitMessage, "' \n git push origin master \n", sep = "")
+system(command = gitCommand, intern = TRUE)
+
+```
+
+
+## update project for release
+
+```{r update project for release}
+
+readyfunctions <- c(
+    "refs",
+    # "^agreement",
+    # "^competingsurvival",
+    # "^correlation",
+    "^crosstable",
+    # "^decision",
+    # "^decisioncalculator",
+    # "^icccoeff",
+    "^multisurvival",
+    "^oddsratio",
+    # "^pairchi2",
+    "^reportcat",
+    # "^roc",
+    "^statsplot2",
+    "^summarydata",
+    "^survival",
+    "^tableone"
+    # "^tree",
+    # "^utils-pipe"
+    # "^vartree"
+)
+
+
+readyfunctions <- paste0(readyfunctions, collapse = "|")
+
+files_R <-
+    list.files(path = here::here("R"),
+               pattern = readyfunctions,
+               full.names = TRUE)
+
+files_jamovi <-
+    list.files(
+        path = here::here("jamovi"),
+        pattern = readyfunctions,
+        full.names = TRUE
+    )
+
+files_data <-
+    list.files(
+        path = here::here("data"),
+        full.names = TRUE
+    )
+
+
+file.copy(from = files_R,
+          to = "~/ClinicoPath/R/",
+          overwrite = TRUE)
+
+
+file.copy(from = files_jamovi,
+          to = "~/ClinicoPath/jamovi/",
+          overwrite = TRUE)
+
+
+file.copy(from = files_data,
+          to = "~/ClinicoPath/data/",
+          overwrite = TRUE)
+
+file.copy(from = files_data,
+          to = "~/histopathRprojects/ClinicoPath/inst/extdata/",
+          overwrite = TRUE)
 
-```{r}
-data('histopathology')
-dat <- as.data.frame(histopathology)
-ClinicoPath::tableone(
-data = dat,
-vars = vars(Sex, PreinvasiveComponent, LVI, PNI, Grade, Age),
-sty = "t2",
-excl = TRUE)
 ```
 
 
@@ -1033,7 +1103,7 @@ deneme <- readxl::read_xlsx(path = here::here("tododata", "histopathology-templa
 ```
 
 
-```{r}
+```{r report}
 deneme <- readxl::read_xlsx(path = here::here("tododata", "histopathology-template2019-11-25.xlsx"))
 
 library(magrittr)
@@ -1052,11 +1122,11 @@ corx <- deneme %>%
 
 
 
-```{r}
+```{r inherits}
 inherits(deneme$Sex, "character")
 ```
 
-```{r}
+```{r betweenstats}
 ggstatsplot::ggbetweenstats(data = deneme,
                             x = Sex,
                             y = Age,
@@ -1491,16 +1561,6 @@ plot <-
 
 # Other Codes
 
-## force git
-
-```{r force git, eval=FALSE, include=FALSE}
-# gitUpdateCommitPush
-CommitMessage <- paste("updated on ", Sys.time(), sep = "")
-wd <- getwd()
-gitCommand <- paste("cd ", wd, " \n git add . \n git commit --message '", CommitMessage, "' \n git push origin master \n", sep = "")
-system(command = gitCommand, intern = TRUE)
-
-```
 
 
 ## arsenal
@@ -2187,76 +2247,6 @@ https://towardsdatascience.com/rtest-pretty-testing-of-r-packages-50f50b135650
 
 
 
-```{r update project for release}
-
-readyfunctions <- c(
-    "refs",
-    # "^agreement",
-    # "^competingsurvival",
-    # "^correlation",
-    "^crosstable",
-    # "^decision",
-    # "^decisioncalculator",
-    # "^icccoeff",
-    # "^multisurvival",
-    # "^oddsratio",
-    # "^pairchi2",
-    "^reportcat",
-    # "^roc",
-    "^statsplot2",
-    "^summarydata",
-    # "^survival",
-    "^tableone"
-    # "^tree",
-    # "^utils-pipe"
-    # "^vartree"
-)
-
-
-readyfunctions <- paste0(readyfunctions, collapse = "|")
-
-files_R <-
-    list.files(path = here::here("R"),
-               pattern = readyfunctions,
-               full.names = TRUE)
-
-files_jamovi <-
-    list.files(
-        path = here::here("jamovi"),
-        pattern = readyfunctions,
-        full.names = TRUE
-    )
-
-files_data <-
-    list.files(
-        path = here::here("data"),
-        full.names = TRUE
-    )
-
-
-file.copy(from = files_R,
-          to = "~/ClinicoPath/R/",
-          overwrite = TRUE)
-
-
-file.copy(from = files_jamovi,
-          to = "~/ClinicoPath/jamovi/",
-          overwrite = TRUE)
-
-
-file.copy(from = files_data,
-          to = "~/ClinicoPath/data/",
-          overwrite = TRUE)
-
-file.copy(from = files_data,
-          to = "~/histopathRprojects/ClinicoPath/inst/extdata/",
-          overwrite = TRUE)
-
-```
-
-
-
-
 
 
 ```{r decision}