update workshop list

Author: SchmidtPaul

.Rhistory

@@ -1,93 +1,3 @@
-filter(group=="block") %>%
-mutate(grp = str_remove(term, "var_")) %>%
-select(group, grp, estimate) %>%
-rename(variance = estimate,
-effect = group)
-,
-diag_lme$modelStruct$varStruct %>%
-coef(unconstrained = FALSE, allCoef = TRUE) %>%
-enframe(name = "grp", value = "varStruct") %>%
-mutate(sigma         = diag_lme$sigma) %>%
-mutate(StandardError = sigma * varStruct) %>%
-mutate(variance      = StandardError ^ 2) %>%
-mutate(effect = "Residual") %>%
-select(effect, grp, variance)
-)
-bind_rows(
-diag_glmmTMB %>%
-tidy(effects = "ran_pars", scales = "vcov") %>%
-filter(group == "block") %>%
-mutate(grp = str_remove(term, "var__")) %>%
-select(group, grp, estimate) %>%
-rename(variance = estimate,
-effect = group)
-,
-diag_glmmTMB %>%
-mixedup::extract_cor_structure(which_cor="diag") %>%
-pivot_longer( cols = 2:3, values_to ="variance", names_to="grp") %>%
-rename(effect = group)
-)
-bind_rows(
-diag_lme %>%
-tidy(effects = "ran_pars", scales = "vcov") %>%
-filter(group=="block") %>%
-mutate(grp = str_remove(term, "var_")) %>%
-select(group, grp, estimate) %>%
-rename(variance = estimate,
-effect = group)
-,
-diag_lme$modelStruct$varStruct %>%
-coef(unconstrained = FALSE, allCoef = TRUE) %>%
-enframe(name = "grp", value = "varStruct") %>%
-mutate(sigma         = diag_lme$sigma) %>%
-mutate(StandardError = sigma * varStruct) %>%
-mutate(variance      = StandardError ^ 2) %>%
-mutate(effect = "Residual") %>%
-select(effect, grp, variance)
-)
-bind_rows(
-diag_glmmTMB %>%
-tidy(effects = "ran_pars", scales = "vcov") %>%
-filter(group == "block") %>%
-mutate(grp = str_remove(term, "var__")) %>%
-select(group, grp, estimate) %>%
-rename(variance = estimate,
-effect = group)
-,
-diag_glmmTMB %>%
-mixedup::extract_cor_structure(which_cor="diag") %>%
-pivot_longer( cols = 2:3, values_to ="variance", names_to="grp") %>%
-rename(effect = group)
-)
-diag_glmmTMB %>%
-mixedup::extract_cor_structure(which_cor="diag")
-bind_rows(
-diag_glmmTMB %>%
-tidy(effects = "ran_pars", scales = "vcov") %>%
-filter(group == "block") %>%
-mutate(grp = str_remove(term, "var__")) %>%
-select(group, grp, estimate) %>%
-rename(variance = estimate,
-effect = group)
-,
-diag_glmmTMB %>%
-mixedup::extract_cor_structure(which_cor="diag", scales = "vcov") %>%
-pivot_longer( cols = 2:3, values_to ="variance", names_to="grp") %>%
-rename(effect = group)
-)
-bind_rows(
-diag_glmmTMB %>%
-tidy(effects = "ran_pars", scales = "vcov") %>%
-filter(group == "block") %>%
-mutate(grp = str_remove(term, "var__")) %>%
-select(group, grp, estimate) %>%
-rename(variance = estimate,
-effect = group)
-,
-diag_glmmTMB %>%
-mixedup::extract_cor_structure(which_cor="diag") %>%
-mutate(estimate = estimate ^2) %>%
-pivot_longer( cols = 2:3, values_to ="variance", names_to="grp") %>%
 rename(effect = group)
 )
 diag_glmmTMB %>%
@@ -510,3 +420,93 @@ knitr::purl(input  = purl_files %>% slice(i) %>% pull(Rmd),
 output = purl_files %>% slice(i) %>% pull(R),
 documentation = 0)
 }
+pacman::p_load(conflicted,
+tidyverse,
+nlme, glmmTMB,
+broom.mixed,
+emo, flair)
+# package function conflicts
+conflict_prefer("filter", "dplyr")
+pacman::p_load(kableExtra)
+options(knitr.kable.NA = '')
+# this is never seen but needed for code below
+dat <- iris %>%
+mutate(unit = 1:n() %>% as.factor()) %>%
+rename(y=Sepal.Length,
+fixedeffects=Species,
+randomeffects=Sepal.Width) %>%
+as_tibble()
+# Chunk 1
+pacman::p_load(conflicted,
+tidyverse,
+nlme, glmmTMB,
+broom.mixed,
+emo, flair)
+# package function conflicts
+conflict_prefer("filter", "dplyr")
+# Chunk 2
+pacman::p_load(kableExtra)
+options(knitr.kable.NA = '')
+# Chunk 3: hideme
+# this is never seen but needed for code below
+dat <- iris %>%
+mutate(unit = 1:n() %>% as.factor()) %>%
+rename(y=Sepal.Length,
+fixedeffects=Species,
+randomeffects=Sepal.Width) %>%
+as_tibble()
+# Chunk 4: StandErrMod
+#
+#
+StandErrMod <- glmmTMB(
+y ~
+fixedeffects +
+(1 | randomeffects),
+REML = TRUE,
+data = dat
+)
+# Chunk 5
+decorate("StandErrMod")
+# Chunk 6: PseudErrMod
+dat <- dat %>%
+mutate(unit = as.factor(1:n()))
+PseudErrMod <- glmmTMB(
+y ~
+fixedeffects +
+(1 | randomeffects) +
+(1 | unit),      # Pseudo Err
+dispformula = ~ 0, # ErrVar = 0
+REML = TRUE,
+data = dat
+)
+decorate("PseudErrMod") %>% flair_lines(c(1,2,8,9))
+purl_files <- list.files(pattern = ".Rmd") %>%
+tibble(Rmd = .) %>%
+filter(Rmd %not_in% c("_hilang_setup.Rmd",
+"0contactinfo.Rmd",
+"index.Rmd",
+"model_selection.Rmd",
+"sources.Rmd",
+"variance_structures.Rmd",
+"weighted_two_stage.Rmd")) %>%
+mutate(R = paste0("Rpurl/",str_sub(Rmd, 1, -3)))
+setwd("D:/Coding/MMFAIR")
+library("rmarkdown")
+`%not_in%` = Negate(`%in%`)
+### create purled R files ###
+purl_files <- list.files(pattern = ".Rmd") %>%
+tibble(Rmd = .) %>%
+filter(Rmd %not_in% c("_hilang_setup.Rmd",
+"0contactinfo.Rmd",
+"index.Rmd",
+"model_selection.Rmd",
+"sources.Rmd",
+"variance_structures.Rmd",
+"weighted_two_stage.Rmd")) %>%
+mutate(R = paste0("Rpurl/",str_sub(Rmd, 1, -3)))
+for(i in 1:nrow(purl_files)){
+knitr::purl(input  = purl_files %>% slice(i) %>% pull(Rmd),
+output = purl_files %>% slice(i) %>% pull(R),
+documentation = 0)
+}
+purl_files

.Rproj.user/6F6C4B3A/pcs/source-pane.pper

@@ -1,3 +1,3 @@
 {
-    "activeTab" : 3
+    "activeTab" : 6
 }

.Rproj.user/6F6C4B3A/rmd-outputs

@@ -1,7 +1,7 @@
-D:/Coding/MMFAIR/autoregressive_time_series.html
-D:/Coding/MMFAIR/heterogeneous_error_variance.html
-
-D:/Coding/MMFAIR/index.html
+D:/Coding/MMFAIR/glmmtmbdispformula0.html
+D:/Coding/MMFAIR/glmmtmbdispformula0.html
+D:/Coding/MMFAIR/glmmtmbdispformula0.html
+D:/Coding/MMFAIR/glmmtmbdispformula0.html
 
 
 

.Rproj.user/6F6C4B3A/sources/prop/4566BC63

@@ -1,4 +1,4 @@
 {
-    "cursorPosition" : "26,0",
-    "scrollLine" : "8"
+    "cursorPosition" : "8,0",
+    "scrollLine" : "0"
 }

.Rproj.user/6F6C4B3A/sources/prop/C5272C1D

@@ -1,5 +1,5 @@
 {
     "cursorPosition" : "10,3",
-    "scrollLine" : "8",
+    "scrollLine" : "0",
     "tempName" : "Untitled2"
 }

0 render_site.R

@@ -23,4 +23,4 @@ for(i in 1:nrow(purl_files)){
               output = purl_files %>% slice(i) %>% pull(R),
               documentation = 0)
 
-}
+}

0contactinfo.Rmd

@@ -91,6 +91,11 @@ Websites </br>
 <i class="fa fa-window-maximize" style="color: #003f75ff;">
 </i> CrashcouRse: R für Bio- und Agrarwissenschaftler </a> </br>
 
+R-packages </br>
+<a href="https://schmidtpaul.github.io/CitaviR/">
+<img src="https://raw.githubusercontent.com/SchmidtPaul/CitaviR/master/docs/favicon-32x32.png" width=16 height=16/>
+</i> CitaviR: A set of tools for dealing with Citavi data </a> </br>
+
 </p>
 
 ```{r text, echo=FALSE, warning=FALSE, message=FALSE}