diff --git a/NEWS.md b/NEWS.md
index 9f31103b..40ea46ef 100644
--- 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
+
+
+
+
diff --git a/README.Rmd b/README.Rmd
index f01d6cbf..181a1d89 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -220,6 +220,11 @@ https://osf.io/9szud/
#### Odds Ratio Table and Plot
+
+
+
+
+
#### Competing Survival
@@ -349,8 +354,9 @@ See https://github.com/ClinicoPath for forked packages.
---
-
-
Buy me a coffee
+
+
+Buy me a coffee
https://paypal.me/serdarbalci
@@ -474,3 +480,8 @@ https://paypal.me/serdarbalci
[](https://github.com/sbalci/clinicopathjamovimodule/issues)
+
+## Videos
+
+
+
diff --git a/data/histopathologyanalysis.omv b/data/histopathologyanalysis.omv
index a01921e9..890200f7 100644
Binary files a/data/histopathologyanalysis.omv and b/data/histopathologyanalysis.omv differ
diff --git a/man/figures/jamovi-ClinicoPath-oddsratio.gif b/man/figures/jamovi-ClinicoPath-oddsratio.gif
new file mode 100644
index 00000000..39dacc2b
Binary files /dev/null and b/man/figures/jamovi-ClinicoPath-oddsratio.gif differ
diff --git a/tododata/todo.Rmd b/tododata/todo.Rmd
index 18aadd8c..9b8ea73c 100644
--- 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}