Course material

Author: magnusdv

R/utils.R

@@ -0,0 +1,31 @@
+# Functions for creating links to local files
+# Only used in vignettes!
+formatLink = function(txt, fil = txt, bold = NA, live = TRUE, folder = NULL) {
+  if(is.na(bold))
+    bold = grepl("lect", fil, ignore.case = TRUE)
+
+  if(bold)
+    txt = sprintf("**%s**", txt)
+
+  if(!live)
+    return(txt)
+
+  if(!is.null(folder))
+    fil = file.path(folder, fil)
+
+  if(!isTRUE(file.exists(fil))) {
+    cat("File does not exist locally:", fil, "\n")
+    return(txt)
+  }
+
+  # Formatted link
+  url = "https://raw.githubusercontent.com/magnusdv/pedsuite/master/vignettes/web_only"
+  sprintf('[%s](%s/%s){target="_blank"}', txt, url, fil)
+}
+
+# Factory
+linkFUN = function(folder) {
+  function(txt, fil = txt, bold = NA, live = TRUE) {
+    formatLink(txt, fil, bold, live, folder = folder)
+  }
+}

vignettes/web_only/course-ghep2024.Rmd

@@ -42,64 +42,44 @@ install.packages("pedsuite")
 ## Software preparation: Familias
 Part of the course is based on kinship testing in the Familias software, which can be installed here: https://familias.no/download.
 
-```{r, echo = F}
-courseFolder = "courses/ghep2024"
-
-# Function for creating links to files
-link = function(tit, file = NULL, bold = F, live = T) {
-  if(bold)
-    tit = sprintf("**%s**", tit)
-  
-  if(!live)
-    return(tit)
-
-  locpth = file.path(courseFolder, file)
-  
-  if(!isTRUE(file.exists(locpth))) {
-    cat("File does not exist locally:", locpth, "\n")
-    return(tit)
-  }
-  
-  # Formatted link
-  url = "https://raw.githubusercontent.com/magnusdv/pedsuite/master/vignettes/web_only"
-  sprintf('[%s](%s/%s)', tit, url, locpth)
-}
-```
-```
 
 ## Schedule
 The course runs each Monday of October 2024, from 16 to 20 (CEST). The following schedule is tentative:
 
+```{r, echo = F}
+link = pedsuite:::linkFUN(folder = "courses/ghep2024")
+```
+
 #### Oct 7: Theory of relatedness
-* 16:00--17:00 `r link("Introduction to pedigrees, QuickPed and R", "ghep2024_lecture1_pedigrees.pdf", bold = T)` (MDV)
-* 17:00--17:45 `r link("Exercises", "exercises1.pdf")`. (`r link("Solutions", "solutions1.pdf")`)
+* 16:00--17:00 `r link("Introduction to pedigrees, QuickPed and R", "ghep2024_lecture1_pedigrees.pdf")` (MDV)
+* 17:00--17:45 `r link("Exercises I", "exercises1.pdf")`. (`r link("Solutions", "solutions1.pdf")`)
 * 17:45--18:00 _Break_
-* 18:00--19:00 `r link("Measures of relatedness", "ghep2024_lecture2_coefficients.pdf", bold = T)` (MDV)
-* 19:00--19:45 `r link("Exercises", "exercises2.pdf")`. (`r link("Solutions", "solutions2.pdf")`)
+* 18:00--19:00 `r link("Measures of relatedness", "ghep2024_lecture2_coefficients.pdf")` (MDV)
+* 19:00--19:45 `r link("Exercises II", "exercises2.pdf")`. (`r link("Solutions", "solutions2.pdf")`)
 * 19:45--20:00 Wrap-up
 
 #### Oct 14: Kinship testing
-* 16:00--17:00 `r link("Introduction to forensic kinship testing", "ghep2024_lecture3_testing.pdf", bold = T)` (TE)
-* 17:00--17:45 `r link("Exercises", "exercises3.pdf")`
+* 16:00--17:00 `r link("Introduction to forensic kinship testing", "ghep2024_lecture3_testing.pdf")` (TE)
+* 17:00--17:45 `r link("Exercises III", "exercises3.pdf")`. (`r link("Solutions", "solutions3.pdf")`)
 * 17:45--18:00 _Break_
-* 18:00--19:00 `r link("Kinship testing with Familias", "ghep2024_lecture4_Familias.pdf", bold = T)` (TE)
-* 19:00--19:45 `r link("Exercises", "exercises4.pdf")`. File needed: `r link("kinship-riddle.fam", "kinship-riddle.fam")`
+* 18:00--19:00 `r link("Kinship testing with Familias", "ghep2024_lecture4_Familias.pdf")` (TE)
+* 19:00--19:45 `r link("Exercises IV", "exercises4.pdf")`. File needed: `r link("kinship-riddle.fam")`. (`r link("Solutions", "solutions4.pdf")`)
 * 19:45--20:00 Wrap-up
 
 #### Oct 21: Relatedness inference
-* 16:00--17:00 `r link("Realised relatedness: Why are some siblings more alike than others?", "ghep2024_lecture5_realised.pdf", bold = T, live = F)` (MDV)
-* 17:00--17:45 `r link("Exercises", "exercises5.pdf", live = F)`
+* 16:00--17:00 `r link("Realised relatedness: Why are some siblings more alike than others?", "ghep2024_lecture5_realised.pdf")` (MDV)
+* 17:00--17:45 `r link("Exercises V", "exercises5.pdf")`. (`r link("Solutions", "solutions5.pdf")`)
 * 17:45--18:00 _Break_
-* 18:00--19:00 `r link("Pedigree reconstruction", "ghep2024_lecture6_reconstruction.pdf", bold = T, live = F)` (MDV)
-* 19:00--19:45 `r link("Exercises", "exercises6.pdf", live = F)`
+* 18:00--19:00 `r link("Pedigree reconstruction", "ghep2024_lecture6_reconstruction.pdf")` (MDV)
+* 19:00--19:45 `r link("Exercises VI", "exercises6.pdf")`. (`r link("Solutions", "solutions6.pdf")`)
 * 19:45--20:00 Wrap-up
 
 #### Oct 28: Disaster victim identification
-* 16:00--17:00 `r link("DNA-based disaster victim identification", "ghep2024_lecture7_dvi.pdf", bold = T, live = F)` (TE)
-* 17:00--17:45 `r link("Exercises", "exercises7.pdf", live = F)`
+* 16:00--17:00 `r link("DNA-based disaster victim identification", "ghep2024_lecture7_DVI_Familias.pdf")` (TE)
+* 17:00--17:45 `r link("Exercises VII", "exercises7.pdf")`. Familias file: `r link("planecrash.fam")`.
 * 17:45--18:00 _Break_
-* 18:00--19:00 `r link("Practical DVI with Diviana", "ghep2024_lecture8_diviana.pdf", bold = T, live = F)` (MDV)
-* 19:00--19:45 `r link("Exercises", "exercises8.pdf", live = F)`
+* 18:00--19:00 `r link("Practical DVI with Diviana", "ghep2024_lecture8_diviana.pdf")` (MDV)
+* 19:00--19:45 `r link("Exercises VIII", "exercises8.pdf")`
 * 19:45--20:00 Wrap-up
 
 Comments and questions may be sent to *magnusdv at gmail dot com*.

vignettes/web_only/course-isfg2023.Rmd

@@ -46,21 +46,25 @@ install.packages("pedsuite")
 ## Schedule
 The course runs from 18 to 22 (CEST) each day, with a 15 minute break in the middle. The following schedule is tentative:
 
+```{r, echo = F}
+link = pedsuite:::linkFUN(folder = "courses/isfg2023")
+```
+
 #### Aug 30 (Wednesday) -- Pedigree analysis: Basic
-* 18:00--19:00 Lecture 1. [**Pedigrees and measures of relatedness**](https://github.com/magnusdv/pedsuite/blob/master/vignettes/web_only/courses/isfg2023/Lecture1_pedigrees.pdf) (MDV)
+* 18:00--19:00 `r link("Pedigrees and measures of relatedness", "Lecture1_pedigrees.pdf")` (MDV)
 * 19:00--19:15 Crash course in R (MDV)
-* 19:15--20:00 [Exercise set 1](https://github.com/magnusdv/pedsuite/blob/master/vignettes/web_only/courses/isfg2023/exercises1.pdf)
+* 19:15--20:00 `r link("Exercises I", "exercises1.pdf")`
 * 20:00--20:15 _Break_
-* 20:15--21:00 Lecture 2. [**Kinship testing**](https://github.com/magnusdv/pedsuite/blob/master/vignettes/web_only/courses/isfg2023/Lecture2_kinship.pdf) (TE)
-* 21:00--21:45 [Exercise set 2](https://github.com/magnusdv/pedsuite/blob/master/vignettes/web_only/courses/isfg2023/exercises2.pdf)
+* 20:15--21:00 `r link("Kinship testing", "Lecture2_kinship.pdf")` (TE)
+* 21:00--21:45 `r link("Exercises II", "exercises2.pdf")`
 * 21:45--22:00 Summary and discussion
 
 #### Aug 31 (Thursday) -- Pedigree analysis: Advanced
-* 18:00--19:00 Lecture 3. [**Relatedness inference and pedigree reconstruction**](https://github.com/magnusdv/pedsuite/blob/master/vignettes/web_only/courses/isfg2023/Lecture3_reconstruction.pdf) (MDV)
-* 19:00--19:45 [Exercise set 3](https://github.com/magnusdv/pedsuite/blob/master/vignettes/web_only/courses/isfg2023/exercises3.pdf)
+* 18:00--19:00 `r link("Relatedness inference and pedigree reconstruction", "Lecture3_reconstruction.pdf")` (MDV)
+* 19:00--19:45 `r link("Exercises III", "exercises3.pdf")`
 * 19:45--20:00 _Break_
-* 20:00--21:00 Lecture 4. [**Disaster victim identification**](https://github.com/magnusdv/pedsuite/blob/master/vignettes/web_only/courses/isfg2023/Lecture4_DVI.pdf) (TE)
-* 21:00--21:45 [Exercise set 4](https://github.com/magnusdv/pedsuite/blob/master/vignettes/web_only/courses/isfg2023/exercises4.pdf)
+* 20:00--21:00 `r link("Disaster victim identification", "Lecture4_DVI.pdf")` (TE)
+* 21:00--21:45 `r link("Exercises IV", "exercises4.pdf")`
 * 21:45--22:00 Summary and discussion
 
 

vignettes/web_only/course-isfg2024.Rmd

@@ -3,7 +3,7 @@ title: ISFG Congress 2024 Workshop
 output: rmarkdown::html_vignette
 vignette: >
   %\VignetteEngine{knitr::rmarkdown}
-  %\VignetteIndexEntry{"Kinship Statistics and Pedigree Analysis"}
+  %\VignetteIndexEntry{ISFG Congress 2024 Workshop}
   %\VignetteEncoding{UTF-8}
 ---
 
@@ -57,23 +57,27 @@ After completing the course the participants will have knowledge about:
 ## Schedule
 The workshop is run as a full-day course on Tuesday 10th, from 9 to 18:30 (CEST). The following schedule is tentative:
 
+```{r, echo = F}
+link = pedsuite:::linkFUN(folder = "courses/isfg2024")
+```
+
 #### Morning session -- Pedigree analysis: Basic
-* 09:00--10:00 Lecture 1. [**Pedigrees and measures of relatedness**](https://github.com/magnusdv/pedsuite/blob/master/vignettes/web_only/courses/isfg2024/Lecture1_pedigrees.pdf) (MDV)
-* 10:00--11:00 [Exercise set 1](https://github.com/magnusdv/pedsuite/blob/master/vignettes/web_only/courses/isfg2024/exercises1.pdf)
+* 09:00--10:00 `r link("Pedigrees and measures of relatedness", "Lecture1_pedigrees.pdf")` (MDV)
+* 10:00--11:00 `r link("Exercises I", "exercises1.pdf")`
 * 11:00--11:15 _Break_
-* 11:15--12:00 Lecture 2. [**Kinship testing**](https://github.com/magnusdv/pedsuite/blob/master/vignettes/web_only/courses/isfg2024/Lecture2-Kinship.pdf) (TE)
-* 12:00--12:45 [Exercise set 2](https://github.com/magnusdv/pedsuite/blob/master/vignettes/web_only/courses/isfg2024/exercises2.pdf)
+* 11:15--12:00 `r link("Kinship testing", "Lecture2-Kinship.pdf")` (TE)
+* 12:00--12:45 `r link("Exercises II", "exercises2.pdf")`
 * 12:45--13:00 Summary and discussion  
 
 
 <p style="text-indent: 12px;">**Lunch break 13:00 - 14:30**</p>
 
 #### Afternoon session -- Pedigree analysis: Advanced
-* 14:30--15:30 Lecture 3. [**Relatedness inference and pedigree reconstruction**](https://github.com/magnusdv/pedsuite/blob/master/vignettes/web_only/courses/isfg2024/Lecture3-reconstruction.pdf) (MDV)
-* 15:30--16:15 [Exercise set 3](https://github.com/magnusdv/pedsuite/blob/master/vignettes/web_only/courses/isfg2024/exercises3.pdf)
+* 14:30--15:30 `r link("Relatedness inference and pedigree reconstruction", "Lecture3-reconstruction.pdf")` (MDV)
+* 15:30--16:15 `r link("Exercises III", "exercises3.pdf")`
 * 16:15--16:30 _Break_
-* 16:30--17:30 Lecture 4. [**Disaster victim identification**](https://github.com/magnusdv/pedsuite/blob/master/vignettes/web_only/courses/isfg2024/Lecture4-DVI.pdf) (TE)
-* 17:30--18:15 [Exercise set 4](https://github.com/magnusdv/pedsuite/blob/master/vignettes/web_only/courses/isfg2024/exercises4.pdf)
+* 16:30--17:30 `r link("Disaster victim identification", "Lecture4-DVI.pdf")` (TE)
+* 17:30--18:15 `r link("Exercises IV", "exercises4.pdf")`
 * 18:15--18:30 Summary and discussion
 
 

vignettes/web_only/course-yid2024.Rmd

@@ -14,30 +14,6 @@ knitr::opts_chunk$set(echo = TRUE,
                       comment = "#>")
 ```
 
-```{r, echo = F}
-courseFolder = "courses/yid2024"
-
-# Function for creating links to files
-link = function(tit, file = NULL, bold = F, live = T) {
-  if(bold)
-    tit = sprintf("**%s**", tit)
-  
-  if(!live)
-    return(tit)
-
-  locpth = file.path(courseFolder, file)
-  
-  if(!isTRUE(file.exists(locpth))) {
-    cat("File does not exist locally:", locpth, "\n")
-    return(tit)
-  }
-  
-  # Formatted link
-  url = "https://raw.githubusercontent.com/magnusdv/pedsuite/master/vignettes/web_only"
-  sprintf('[%s](%s/%s){target="_blank"}', tit, url, locpth)
-}
-```
-
 # Workshop: Genetic relatedness
 
 * Date: Monday 14th of October, 2024
@@ -74,11 +50,15 @@ After completing the course the participants will have knowledge about:
 ## Schedule
 The workshop is run as a half-day course, from 12 to 16, with the following (tentative) schedule:
 
-* 12:00--13:00 Lecture 1. `r link("Introduction to pedigrees and relationships", "yid2024_lecture1_pedigrees.pdf", bold = T)`
-* 13:00--13:45 `r link("Exercises", "exercises1.pdf")` <!--. (`r link("Solutions", "solutions1.pdf")`) -->
+```{r, echo = F}
+link = pedsuite:::linkFUN(folder = "courses/yid2024")
+```
+
+* 12:00--13:00 `r link("Introduction to pedigrees and relationships", "yid2024_lecture1_pedigrees.pdf")`
+* 13:00--13:45 `r link("Exercises I", "exercises1.pdf")`. (`r link("Solutions", "solutions1.pdf")`)
 * 13:45--14:00 _Break_
-* 14:00--15:00 Lecture 2. `r link("Measures of relatedness", "yid2024_lecture2_coefficients.pdf", bold = T)`
-* 15:00--15:45 `r link("Exercises", "exercises2.pdf")` <!--.. (`r link("Solutions", "solutions2.pdf")`) -->
+* 14:00--15:00 `r link("Measures of relatedness", "yid2024_lecture2_coefficients.pdf")`
+* 15:00--15:45 `r link("Exercises II", "exercises2.pdf")`. (`r link("Solutions", "solutions2.pdf")`)
 * 15:45--16:00 Summary and discussion  
 
 Comments and questions may be sent to *magnusdv at gmail dot com*.

vignettes/web_only/courses.Rmd

@@ -12,21 +12,23 @@ knitr::opts_chunk$set(echo = FALSE,
                       fig.align = "center",
                       collapse = TRUE,
                       comment = "#>")
-```
 
-## Upcoming stuff
+formatLink = pedsuite:::formatLink
+```
 
-* Oct 14, 2024 **Genetic Relatedness**. Half-day workshop at the *Young Investigator Day* at the [NOFE Conference](https://nofe.no/nofe-conference-2024/). Lecturer: Magnus D. Vigeland. [Course homepage](https://magnusdv.github.io/pedsuite/articles/web_only/course-yid2024.html).
+## Upcoming events
 
-* Oct 10, 2024. **DIVIANA: A free, user-friendly app for complex DVI cases**. Invited online talk at the _2nd International Symposium on DNA Supported Missing Persons and Disaster Victim Identification_, Tbilisi, Georgia. Speaker: Magnus D. Vigeland.
-* Oct 7,14,21 and 28, 2024 **Kinship and pedigree analysis: Methods and applications**. Four-part lecture series, part of the [ISFG-GHEP Online School 2024](https://ghep-isfg.org/en/workshops/ghep-os/autumn2024/WS1/). Teachers: Magnus D. Vigeland and Thore Egeland. [Course homepage](https://magnusdv.github.io/pedsuite/articles/web_only/course-ghep2024.html).
+* Oct 7,14,21 and 28, 2024. **Kinship and pedigree analysis: Methods and applications**. Four-part lecture series, part of the [ISFG-GHEP Online School 2024](https://ghep-isfg.org/en/workshops/ghep-os/autumn2024/WS1/). Teachers: Magnus D. Vigeland and Thore Egeland. [Course homepage](https://magnusdv.github.io/pedsuite/articles/web_only/course-ghep2024.html).
 
-## Past stuff
+## Past events
 
 ### 2024
 
-* Sept 24. **Advanced Theoretical Challenges: Kinship**. Presentation of solutions and results for the theoretical proficiency test prepared for ISFG-GHEP 2024. [Exercises](https://github.com/magnusdv/pedsuite/blob/master/vignettes/web_only/GHEP/ghep_kinship24_final_EN.pdf). [Presentation](https://github.com/magnusdv/pedsuite/blob/master/vignettes/web_only/GHEP/ghep-kinship24-presentation.pdf)
-* Sept 11. **DIVIANA: A free, user-friendly app for complex DVI cases**. Oral presentation at the ISFG Congress 2024, Santiago de Compostela. Speaker: Magnus D. Vigeland.
+* Oct 15. **DIVIANA: A free, user-friendly app for complex DVI cases**. Research seminar RMF, Storo, Oslo. Speaker: Magnus D. Vigeland.
+* Oct 14. **Genetic Relatedness**. Half-day workshop at the *Young Investigator Day* at the [NOFE Conference](https://nofe.no/nofe-conference-2024/). Lecturer: Magnus D. Vigeland. [Course homepage](https://magnusdv.github.io/pedsuite/articles/web_only/course-yid2024.html).
+* Oct 10. **DIVIANA: A free, user-friendly app for complex DVI cases**. Invited online talk at the _2nd Intl Symposium on DNA Supported Missing Persons and Disaster Victim Identification_, Tbilisi, Georgia. Speaker: Magnus D. Vigeland. `r formatLink("Slides", "talks/2024-10-10-Tbilisi-DIVIANA.pdf")` (extended version of the ISFG talk).
+* Sept 24. **Advanced Theoretical Challenges: Kinship**. Presentation of solutions and results for the theoretical proficiency test prepared for ISFG-GHEP 2024. `r formatLink("Exercises", "GHEP/ghep_kinship24_final_EN.pdf")`. `r formatLink("Presentation", "GHEP/ghep-kinship24-presentation.pdf")`.
+* Sept 11. **DIVIANA: A free, user-friendly app for complex DVI cases**. Oral presentation at the ISFG Congress 2024, Santiago de Compostela. Speaker: Magnus D. Vigeland. `r formatLink("Slides", "talks/2024-09-11-ISFG-Santiago.pdf")`.
 * Sept 10. **Kinship statistics and pedigree analysis**. Pre-congress workshop, ISFG Congress 2024, Santiago de Compostela. Teachers: Magnus D. Vigeland and Thore Egeland. [Course homepage](https://magnusdv.github.io/pedsuite/articles/web_only/course-isfg2024.html).