reoganize files

nmfs-fish-tools · Oct 19, 2023 · 102aa9d · 102aa9d
1 parent 15dc778
commit 102aa9d
Show file tree

Hide file tree

Showing 38 changed files with 18 additions and 17 deletions.
diff --git a/TextAnalysis/top10_analysis.R → inst/TextAnalysis/top10_analysis.R b/TextAnalysis/top10_analysis.R → inst/TextAnalysis/top10_analysis.R
@@ -214,9 +214,9 @@ proportion_database <- rbind(
 )
 proportion_database[nrow(proportion_database), "ID"] <- "Sum"
 
-write.csv(frequency_database, file=here::here("TextAnalysis", "top10_frequency.csv"), row.names=FALSE)
-write.csv(presence_database, file=here::here("TextAnalysis", "top10_presence.csv"), row.names=FALSE)
-write.csv(proportion_database, file=here::here("TextAnalysis", "top10_proportion.csv"), row.names=FALSE)
+write.csv(frequency_database, file=here::here("inst", "TextAnalysis", "top10_frequency.csv"), row.names=FALSE)
+write.csv(presence_database, file=here::here("inst", "TextAnalysis", "top10_presence.csv"), row.names=FALSE)
+write.csv(proportion_database, file=here::here("inst","TextAnalysis", "top10_proportion.csv"), row.names=FALSE)
 
 # Upload xlsx to Google Drive
 authorize_GoogleDrive <- FALSE
@@ -227,9 +227,9 @@ if (authorize_GoogleDrive) {
 }
 
 # Plot results ------------------------------------------------------------
-frequency_database <- read.csv(file=here::here("TextAnalysis", "top10_frequency.csv"))
-presence_database<-read.csv(file=here::here("TextAnalysis", "top10_presence.csv"))
-proportion_database<-read.csv(file=here::here("TextAnalysis", "top10_proportion.csv"))
+frequency_database <- read.csv(file=here::here("inst", "TextAnalysis", "top10_frequency.csv"))
+presence_database<-read.csv(file=here::here("inst", "TextAnalysis", "top10_presence.csv"))
+proportion_database<-read.csv(file=here::here("inst", "TextAnalysis", "top10_proportion.csv"))
 
 colnames(presence_database) <- col_name
 data_reshape <- reshape2::melt(
@@ -244,7 +244,7 @@ sum_by_group <- aggregate(value ~ keyword+keyword_id+group+Source, data = data_m
 sum_by_group <- sum_by_group[order(sum_by_group$keyword_id),]
 group <- unique(sum_by_group$group)
 
-jpeg(filename = here::here("TextAnalysis", "top10_barplot_sum.jpg"), width=200, height=150, units="mm", res=1200)
+jpeg(filename = here::here("inst", "TextAnalysis", "top10_barplot_sum.jpg"), width=200, height=150, units="mm", res=1200)
 ggplot(sum_by_group, aes(fill=Source, y=value, x=keyword_id)) + 
   geom_bar(position="dodge", stat="identity") +
   facet_wrap(~group, scales = "free_x") +
@@ -260,7 +260,7 @@ mean_by_group <- aggregate(value ~ keyword+keyword_id+group+Source, data = data_
 mean_by_group <- mean_by_group[order(mean_by_group$keyword_id),]
 group <- unique(mean_by_group$group)
 
-jpeg(filename = here::here("TextAnalysis", "top10_barplot_mean.jpg"), width=200, height=150, units="mm", res=1200)
+jpeg(filename = here::here("inst", "TextAnalysis", "top10_barplot_mean.jpg"), width=200, height=150, units="mm", res=1200)
 ggplot(mean_by_group, aes(fill=Source, y=value*100, x=keyword_id)) + 
   geom_bar(position="dodge", stat="identity") +
   facet_wrap(~group, scales = "free_x") +

diff --git a/TextAnalysis/top10_barplot_mean.jpg → inst/TextAnalysis/top10_barplot_mean.jpg b/TextAnalysis/top10_barplot_mean.jpg → inst/TextAnalysis/top10_barplot_mean.jpg
diff --git a/TextAnalysis/top10_barplot_sum.jpg → inst/TextAnalysis/top10_barplot_sum.jpg b/TextAnalysis/top10_barplot_sum.jpg → inst/TextAnalysis/top10_barplot_sum.jpg
diff --git a/TextAnalysis/top10_frequency.csv → inst/TextAnalysis/top10_frequency.csv b/TextAnalysis/top10_frequency.csv → inst/TextAnalysis/top10_frequency.csv
diff --git a/TextAnalysis/top10_presence.csv → inst/TextAnalysis/top10_presence.csv b/TextAnalysis/top10_presence.csv → inst/TextAnalysis/top10_presence.csv
diff --git a/TextAnalysis/top10_proportion.csv → inst/TextAnalysis/top10_proportion.csv b/TextAnalysis/top10_proportion.csv → inst/TextAnalysis/top10_proportion.csv
diff --git a/TextAnalysis/top20_analysis.R → inst/TextAnalysis/top20_analysis.R b/TextAnalysis/top20_analysis.R → inst/TextAnalysis/top20_analysis.R
@@ -223,9 +223,9 @@ for (org in seq_along(subfolder_info)){
   )
   proportion_database[nrow(proportion_database), "ID"] <- "Sum"
 
-  write.csv(frequency_database, file=here::here("TextAnalysis", paste0("top20_frequency_", names(subfolder_info)[org], ".csv")), row.names=FALSE)
-  write.csv(presence_database, file=here::here("TextAnalysis", paste0("top20_presence_", names(subfolder_info)[org], ".csv")), row.names=FALSE)
-  write.csv(proportion_database, file=here::here("TextAnalysis", paste0("top20_proportion_", names(subfolder_info)[org], ".csv")), row.names=FALSE)
+  write.csv(frequency_database, file=here::here("inst", "TextAnalysis", paste0("top20_frequency_", names(subfolder_info)[org], ".csv")), row.names=FALSE)
+  write.csv(presence_database, file=here::here("inst", "TextAnalysis", paste0("top20_presence_", names(subfolder_info)[org], ".csv")), row.names=FALSE)
+  write.csv(proportion_database, file=here::here("inst", "TextAnalysis", paste0("top20_proportion_", names(subfolder_info)[org], ".csv")), row.names=FALSE)
   # Upload xlsx to Google Drive
   if (authorize_GoogleDrive) {
     # Google Drive folder id
@@ -234,9 +234,9 @@ for (org in seq_along(subfolder_info)){
   }
 
   # Plot results ------------------------------------------------------------
-  frequency_database <- read.csv(file=here::here("TextAnalysis", paste0("top20_frequency_", names(subfolder_info)[org], ".csv")))
-  presence_database<-read.csv(file=here::here("TextAnalysis", paste0("top20_presence_", names(subfolder_info)[org], ".csv")))
-  proportion_database<-read.csv(file=here::here("TextAnalysis", paste0("top20_proportion_", names(subfolder_info)[org], ".csv")))
+  frequency_database <- read.csv(file=here::here("inst", "TextAnalysis", paste0("top20_frequency_", names(subfolder_info)[org], ".csv")))
+  presence_database<-read.csv(file=here::here("inst", "TextAnalysis", paste0("top20_presence_", names(subfolder_info)[org], ".csv")))
+  proportion_database<-read.csv(file=here::here("inst", "TextAnalysis", paste0("top20_proportion_", names(subfolder_info)[org], ".csv")))
 
   word_frequency <- as.matrix(frequency_database[frequency_database$ID == "Sum", 4:ncol(frequency_database)])
   word_presence <- as.matrix(presence_database[presence_database$ID == "Sum", 4:ncol(presence_database)])
@@ -266,7 +266,7 @@ for (org in seq_along(subfolder_info)){
   )
 
   # barplot
-  jpeg(filename = here::here("TextAnalysis", paste0("top20_barplot_", names(subfolder_info)[org], ".jpg")), width = 200, height = 120, units = "mm", res = 1200)
+  jpeg(filename = here::here("inst", "TextAnalysis", paste0("top20_barplot_", names(subfolder_info)[org], ".jpg")), width = 200, height = 120, units = "mm", res = 1200)
   par(mar = c(6, 4, 1, 1), mfrow = c(3, 1))
   frequency_barplot <- barplot(height = word_frequency, xaxt = "n", ylab = "Frequency")
   text(frequency_barplot - 0.25, par("usr")[3] - 0.25, xlabels, xpd = TRUE, srt = 40, adj = 1, cex = 0.8)
@@ -280,14 +280,14 @@ for (org in seq_along(subfolder_info)){
 
   dev.off()
 
-  jpeg(filename = here::here("TextAnalysis", paste0("top20_presence_", names(subfolder_info)[org], ".jpg")), width = 200, height = 120, units = "mm", res = 1200)
+  jpeg(filename = here::here("inst", "TextAnalysis", paste0("top20_presence_", names(subfolder_info)[org], ".jpg")), width = 200, height = 120, units = "mm", res = 1200)
   par(mar = c(6, 4, 1, 1), mfrow = c(1, 1))
   presence_barplot <- barplot(height = word_presence, xaxt = "n", ylab = "Frequency") # range: 26-83, median:68
   text(presence_barplot - 0.25, par("usr")[3] - 0.25, xlabels, xpd = TRUE, srt = 40, adj = 1, cex = 0.7)
   dev.off()
 
   # wordcloud figure
-  jpeg(filename = here::here("TextAnalysis", paste0("top20_wordcloud_", names(subfolder_info)[org], ".jpg")), width = 200, height = 200, units = "mm", res = 1200)
+  jpeg(filename = here::here("inst", "TextAnalysis", paste0("top20_wordcloud_", names(subfolder_info)[org], ".jpg")), width = 200, height = 200, units = "mm", res = 1200)
   par(mar = c(1, 1, 1, 1), mfrow = c(1, 1))
   wordcloud(
     words = xlabels, freq = word_presence, rot.per = 0.35,

diff --git a/TextAnalysis/top20_barplot_All.jpg → inst/TextAnalysis/top20_barplot_All.jpg b/TextAnalysis/top20_barplot_All.jpg → inst/TextAnalysis/top20_barplot_All.jpg
diff --git a/TextAnalysis/top20_barplot_Australia.jpg → .../TextAnalysis/top20_barplot_Australia.jpg b/TextAnalysis/top20_barplot_Australia.jpg → .../TextAnalysis/top20_barplot_Australia.jpg
diff --git a/TextAnalysis/top20_barplot_ICES.jpg → inst/TextAnalysis/top20_barplot_ICES.jpg b/TextAnalysis/top20_barplot_ICES.jpg → inst/TextAnalysis/top20_barplot_ICES.jpg
diff --git a/TextAnalysis/top20_barplot_NOAA.jpg → inst/TextAnalysis/top20_barplot_NOAA.jpg b/TextAnalysis/top20_barplot_NOAA.jpg → inst/TextAnalysis/top20_barplot_NOAA.jpg
diff --git a/TextAnalysis/top20_frequency_All.csv → inst/TextAnalysis/top20_frequency_All.csv b/TextAnalysis/top20_frequency_All.csv → inst/TextAnalysis/top20_frequency_All.csv
diff --git a/TextAnalysis/top20_frequency_Australia.csv → ...extAnalysis/top20_frequency_Australia.csv b/TextAnalysis/top20_frequency_Australia.csv → ...extAnalysis/top20_frequency_Australia.csv
diff --git a/TextAnalysis/top20_frequency_ICES.csv → inst/TextAnalysis/top20_frequency_ICES.csv b/TextAnalysis/top20_frequency_ICES.csv → inst/TextAnalysis/top20_frequency_ICES.csv
diff --git a/TextAnalysis/top20_frequency_NOAA.csv → inst/TextAnalysis/top20_frequency_NOAA.csv b/TextAnalysis/top20_frequency_NOAA.csv → inst/TextAnalysis/top20_frequency_NOAA.csv
diff --git a/TextAnalysis/top20_presence_All.csv → inst/TextAnalysis/top20_presence_All.csv b/TextAnalysis/top20_presence_All.csv → inst/TextAnalysis/top20_presence_All.csv
diff --git a/TextAnalysis/top20_presence_All.jpg → inst/TextAnalysis/top20_presence_All.jpg b/TextAnalysis/top20_presence_All.jpg → inst/TextAnalysis/top20_presence_All.jpg
diff --git a/TextAnalysis/top20_presence_Australia.csv → ...TextAnalysis/top20_presence_Australia.csv b/TextAnalysis/top20_presence_Australia.csv → ...TextAnalysis/top20_presence_Australia.csv
diff --git a/TextAnalysis/top20_presence_Australia.jpg → ...TextAnalysis/top20_presence_Australia.jpg b/TextAnalysis/top20_presence_Australia.jpg → ...TextAnalysis/top20_presence_Australia.jpg
diff --git a/TextAnalysis/top20_presence_ICES.csv → inst/TextAnalysis/top20_presence_ICES.csv b/TextAnalysis/top20_presence_ICES.csv → inst/TextAnalysis/top20_presence_ICES.csv
diff --git a/TextAnalysis/top20_presence_ICES.jpg → inst/TextAnalysis/top20_presence_ICES.jpg b/TextAnalysis/top20_presence_ICES.jpg → inst/TextAnalysis/top20_presence_ICES.jpg
diff --git a/TextAnalysis/top20_presence_NOAA.csv → inst/TextAnalysis/top20_presence_NOAA.csv b/TextAnalysis/top20_presence_NOAA.csv → inst/TextAnalysis/top20_presence_NOAA.csv
diff --git a/TextAnalysis/top20_presence_NOAA.jpg → inst/TextAnalysis/top20_presence_NOAA.jpg b/TextAnalysis/top20_presence_NOAA.jpg → inst/TextAnalysis/top20_presence_NOAA.jpg
diff --git a/TextAnalysis/top20_proportion_All.csv → inst/TextAnalysis/top20_proportion_All.csv b/TextAnalysis/top20_proportion_All.csv → inst/TextAnalysis/top20_proportion_All.csv
diff --git a/TextAnalysis/top20_proportion_Australia.csv → ...xtAnalysis/top20_proportion_Australia.csv b/TextAnalysis/top20_proportion_Australia.csv → ...xtAnalysis/top20_proportion_Australia.csv
diff --git a/TextAnalysis/top20_proportion_ICES.csv → inst/TextAnalysis/top20_proportion_ICES.csv b/TextAnalysis/top20_proportion_ICES.csv → inst/TextAnalysis/top20_proportion_ICES.csv
diff --git a/TextAnalysis/top20_proportion_NOAA.csv → inst/TextAnalysis/top20_proportion_NOAA.csv b/TextAnalysis/top20_proportion_NOAA.csv → inst/TextAnalysis/top20_proportion_NOAA.csv
diff --git a/TextAnalysis/top20_wordcloud_All.jpg → inst/TextAnalysis/top20_wordcloud_All.jpg b/TextAnalysis/top20_wordcloud_All.jpg → inst/TextAnalysis/top20_wordcloud_All.jpg
diff --git a/TextAnalysis/top20_wordcloud_Australia.jpg → ...extAnalysis/top20_wordcloud_Australia.jpg b/TextAnalysis/top20_wordcloud_Australia.jpg → ...extAnalysis/top20_wordcloud_Australia.jpg
diff --git a/TextAnalysis/top20_wordcloud_ICES.jpg → inst/TextAnalysis/top20_wordcloud_ICES.jpg b/TextAnalysis/top20_wordcloud_ICES.jpg → inst/TextAnalysis/top20_wordcloud_ICES.jpg
diff --git a/TextAnalysis/top20_wordcloud_NOAA.jpg → inst/TextAnalysis/top20_wordcloud_NOAA.jpg b/TextAnalysis/top20_wordcloud_NOAA.jpg → inst/TextAnalysis/top20_wordcloud_NOAA.jpg
diff --git a/TextAnalysis/tree.txt → inst/TextAnalysis/tree.txt b/TextAnalysis/tree.txt → inst/TextAnalysis/tree.txt
diff --git a/emltest.R → inst/examples/emltest.R b/emltest.R → inst/examples/emltest.R
diff --git a/example.R → inst/examples/example.R b/example.R → inst/examples/example.R
diff --git a/test.R → inst/examples/test.R b/test.R → inst/examples/test.R
diff --git a/text_mining.R → inst/examples/text_mining.R b/text_mining.R → inst/examples/text_mining.R
diff --git a/_pkgdown.yml → pkgdown/_pkgdown.yml b/_pkgdown.yml → pkgdown/_pkgdown.yml
@@ -33,6 +33,7 @@ reference:
   - read_in
   - shiny_dd
   - validate_Rd
+  - make_hex
 
 
 navbar:

diff --git a/extra.css → pkgdown/extra.css b/extra.css → pkgdown/extra.css
-Original file line number
+Diff line change
@@ Expand Up / @@ -33,6 +33,7 @@ reference: @@
       - read_in
       - shiny_dd
       - validate_Rd
+      - make_hex
     navbar:
@@ Expand Down @@