Erarr dev (#36)

v. 0.1.3 * fixed naming bug * tweaked milestone plot width * fixed milestoneplot function --------- Co-authored-by: Michael Dougherty <[email protected]>
MVR-GIS · Oct 30, 2024 · 3dfd72b · 3dfd72b
1 parent f9cb82b
commit 3dfd72b
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diff --git a/.Rprofile b/.Rprofile
@@ -0,0 +1 @@
+source("renv/activate.R")
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: erarr
 Title: A package to support the Enterprise Risk Analysis Reporting
     Application
-Version: 0.1.2
+Version: 0.1.3
 Authors@R: c(
     person("Barrie", "Chileen Martinez", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-6960-8167")),
@@ -38,9 +38,7 @@ Imports:
     shinyalert,
     shinyjs,
     stringr,
-    tidyr,
-    webshot,
-    usethis
+    tidyr
 Suggests: 
     htmlwidgets,
     spelling,

diff --git a/NAMESPACE b/NAMESPACE
@@ -9,12 +9,7 @@ export(proj_pieprep)
 export(proj_tableprep)
 export(run_app)
 export(update_data)
-import(english)
-import(ggplot2)
-import(ggrepel)
-import(rlang)
 import(shiny)
-import(webshot)
 importFrom(DT,DTOutput)
 importFrom(DT,datatable)
 importFrom(DT,renderDT)
@@ -40,7 +35,6 @@ importFrom(dplyr,slice_head)
 importFrom(dplyr,slice_max)
 importFrom(dplyr,summarise)
 importFrom(dplyr,summarize)
-importFrom(english,english)
 importFrom(forcats,fct_inorder)
 importFrom(formattable,currency)
 importFrom(ggplot2,aes)
@@ -63,7 +57,6 @@ importFrom(golem,with_golem_options)
 importFrom(kableExtra,kable_styling)
 importFrom(kableExtra,kbl)
 importFrom(knitr,include_graphics)
-importFrom(knitr,kable)
 importFrom(plotly,add_pie)
 importFrom(plotly,layout)
 importFrom(plotly,plot_ly)

diff --git a/R/milestoneplot.R b/R/milestoneplot.R
@@ -40,7 +40,7 @@ mileplot <- ggplot(projphases,
              shape = 21, stroke = .75) +
   geom_point(aes(x = riskitem$PROJECTMILESTONEID, y = 0.1), 
              colour = "#1F78B4", fill = "#1F78B4", shape = 16, size = 4) +
-  geom_text(aes(label = str_wrap(riskitem$MILESTONE, width=14)), 
+  geom_text(aes(label = str_wrap(MILESTONE, width=14)), 
 
             position = position_nudge(y = -0.55), size = 3) +
   scale_y_continuous(limits = c(-1, 1), expand = c(0, 0)) +

diff --git a/R/report_project_Top4s.R b/R/report_project_Top4s.R
@@ -0,0 +1,20 @@
+#' @title Project Top 4 Risks Report
+#' 
+#' @description Creates a report of top 4 risks. 
+#' 
+#' @details All package reports are stored in the folder: `./inst/app/rmd/`
+#' 
+#' @name ProjectTop4s
+#' 
+#' @param projID   character; erisk Project identifier
+#' @param p2ID     numeric; USACE P2 number
+#' @param p2sub    numeric; P2 sub identifier
+#' 
+#' 
+#' 
+#' @importFrom readr read_csv
+#' @importFrom dplyr select mutate filter arrange slice_head
+#' @importFrom formattable currency
+#' @importFrom kableExtra kbl kable_styling
+#' 
+NULL
diff --git a/R/report_project_all_risks.R b/R/report_project_all_risks.R
@@ -11,15 +11,8 @@
 #' @param p2sub    numeric; P2 sub identifier
 #' 
 #' @importFrom readr read_csv
-#' @importFrom dplyr left_join select filter mutate arrange slice_head 
-#'                   case_when
+#' @importFrom dplyr select filter arrange mutate
 #' @importFrom tidyr separate
-#' @importFrom formattable currency
 #' @importFrom kableExtra kbl kable_styling
-#' @import rlang
-#' @import ggplot2
-#' @import ggrepel
-#' @import english
-#' @import webshot
 #' 
 NULL
diff --git a/R/report_risk_item.R b/R/report_risk_item.R
@@ -10,11 +10,10 @@
 #' @param projID   character; erisk Project identifier
 #' @param p2ID     numeric; USACE P2 number
 #' 
-#' @importFrom dplyr left_join mutate select filter case_when slice_max
-#' @importFrom knitr include_graphics kable
+#' @importFrom dplyr mutate select filter left_join case_when slice_max
+#' @importFrom knitr include_graphics 
 #' @importFrom kableExtra kable_styling
 #' @importFrom formattable currency
-#' @importFrom english english
 #' @importFrom stringr str_to_title
 #' @importFrom plotly plot_ly add_pie layout 
 #' @importFrom stringr str_trim

diff --git a/R/wrangle_riskitem_table.R b/R/wrangle_riskitem_table.R
@@ -37,7 +37,6 @@ create_risk_proj <- function(risk, project, archive){
 
   readr::write_csv(risk_item_db,
                    paste0(output_path, "erisk_project_riskitem.csv"))
-  usethis::use_data(risk_item_db, overwrite = TRUE)
 
 return(risk_item_db)
 }
diff --git a/R/wrangle_riskprogram_table.R b/R/wrangle_riskprogram_table.R
@@ -35,6 +35,6 @@ create_risk_prog <- function(erisk_orgs, erisk_dist, erisk_msc, risk_item_db){
                  dplyr::select(MSC, MSC_DESCRIPT, DISTRICT_CODE), by=dplyr::join_by(DISTRICT_CODE), keep=FALSE)
 
   readr::write_csv(risk_program_db, paste0(output_path, "erisk_program_riskitem.csv"))
-  usethis::use_data(risk_program_db, overwrite = TRUE)
 return(risk_program_db)
 }
+
diff --git a/data-raw/Data_Update.Rmd b/data-raw/Data_Update.Rmd
@@ -1,6 +1,6 @@
 ---
-  title: "Update Risk Analysis Report Test Data
-date: "`r Sys.Date()`"
+  title: "Update Risk Analysis Report Test Data"
+  date: `r Sys.Date()`
 ---
 
 # Introduction
@@ -82,6 +82,7 @@ readr::write_csv(erisk_dist,"C:/workspace/erarr/inst/app/data/erisk_dist.csv")
 readr::write_csv(erisk_msc,"C:/workspace/erarr/inst/app/data/erisk_msc.csv")
 readr::write_csv(erisk_modeled,"C:/workspace/erarr/inst/app/data/erisk_modeled.csv")
 
+erisk_item_db <- risk_item_db
 usethis::use_data(erisk_project,
                   erisk_phase_milestone,
                   erisk_item,

diff --git a/data/erisk_item_db.rda b/data/erisk_item_db.rda
diff --git a/data/erisk_phase_milestone.rda b/data/erisk_phase_milestone.rda
diff --git a/data/erisk_program_db.rda b/data/erisk_program_db.rda
diff --git a/data/phase_milestone.rda b/data/phase_milestone.rda
diff --git a/data/risk_item_db.rda b/data/risk_item_db.rda
diff --git a/data/risk_program_db.rda b/data/risk_program_db.rda
diff --git a/dev/01_start.R b/dev/01_start.R
@@ -40,7 +40,7 @@ golem::use_recommended_tests()
 ## Favicon ----
 # If you want to change the favicon (default is golem's one)
 golem::remove_favicon()
-golem::use_favicon(path="inst/app/www/erarr.png")
+golem::use_favicon(path="inst/app/www/castle.png")
 
 
 ## Add helper functions ----

diff --git a/dev/02_dev.R b/dev/02_dev.R
@@ -46,6 +46,8 @@ usethis::use_data(erisk_project,
                   erisk_dist,
                   erisk_msc,
                   erisk_modeled,
+                  erisk_program_riskitem,
+                  erisk_project_riskitem,
                   overwrite = TRUE)
 
 ## Tests ----

diff --git a/inst/app/rmd/ProjectAllRiskReport.Rmd b/inst/app/rmd/ProjectAllRiskReport.Rmd
@@ -39,15 +39,8 @@ body {-webkit-print-color-adjust: exact;}
 ```{r echo=FALSE, message=FALSE, warning=FALSE, include=FALSE}
 library(readr) 
 library(dplyr)
-library(magrittr) 
 library(tidyr)
-library(rlang)
-library(formattable)
-library(plotly)
-library(ggplot2)
-library(ggrepel)
 library(kableExtra)
-library(english)
 ```
 
 ```{r echo=FALSE, message=FALSE, warning=FALSE, include=FALSE}
@@ -56,7 +49,7 @@ risk_item_db<-readr::read_csv("../data/erisk_program_riskitem.csv",
                                  show_col_types = FALSE)
 
 RiskDeets <- risk_item_db |>
-  select("PROJECT_ID", "P2_NUMBER", "RISK_IDENTIFIER", "P2_SUB_IDENTIFIER", 
+  dplyr::select("PROJECT_ID", "P2_NUMBER", "RISK_IDENTIFIER", "P2_SUB_IDENTIFIER", 
          "PROJECT_NAME", "RISK_NAME", "RISKCATEGORY", "RISK_STATEMENT", 
          "LIFECYCLEPHASENAME", "MILESTONE", "LIKELIHOOD", "DISCIPLINE", 
          "PERFORMANCEIMPACT", "PERFORMANCE_RANK_DESC", 
@@ -69,8 +62,8 @@ RiskDeets <- risk_item_db |>
 
 ```{r echo=FALSE, eval = params$projID != ""}
 Risk_List_Proj <- RiskDeets |>
-  filter(RiskDeets$PROJECT_NAME == params$projID)
-proj_risks <- filter(Risk_List_Proj, 
+  dplyr::filter(RiskDeets$PROJECT_NAME == params$projID)
+proj_risks <- dplyr::filter(Risk_List_Proj, 
                      Risk_List_Proj$PROJECT_NAME == params$projID)
 proj_risk_item <- slice_head(Risk_List_Proj)
 header <- paste("Project:", proj_risk_item$PROJECT_NAME)
@@ -79,28 +72,28 @@ header2 <- if (params$p2sub != "") {paste("SubID:", params$p2sub)}
 ```
 
 ```{r echo=FALSE, eval = params$p2ID != ""}
-Risk_List_Proj <- filter(RiskDeets, RiskDeets$P2_NUMBER == params$p2ID)
+Risk_List_Proj <- dplyr::filter(RiskDeets, RiskDeets$P2_NUMBER == params$p2ID)
 
-proj_risks <- filter(Risk_List_Proj, Risk_List_Proj$P2_NUMBER == params$p2ID)
-proj_risk_item <- slice_head(Risk_List_Proj)
+proj_risks <- dplyr::filter(Risk_List_Proj, Risk_List_Proj$P2_NUMBER == params$p2ID)
+proj_risk_item <- dplyr::slice_head(Risk_List_Proj)
 header <- paste("P2 Number:", proj_risk_item$P2_NUMBER)
 header2 <- if (params$p2sub != "") {paste("SubID:", params$p2sub)}
 
 
 ```
 
 ```{r echo=FALSE,  eval = params$p2sub != ""}
-Risk_List_Proj<-filter(Risk_List_Proj,
+Risk_List_Proj<-dplyr::filter(Risk_List_Proj,
                   Risk_List_Proj$P2_SUB_IDENTIFIER == params$p2sub)
-proj_risks <- filter(proj_risks,
+proj_risks <- dplyr::filter(proj_risks,
                      proj_risks$P2_SUB_IDENTIFIER == params$p2sub)
 
 header2 <- if (params$p2sub != "") {paste("SubID:", params$p2sub)}
 ```
 
 ```{r echo=FALSE, message=FALSE, warning=FALSE, include=FALSE}
 proj_risks <- proj_risks %>%
-  mutate(
+  dplyr::mutate(
     'costcolor' = case_when(
       COST_RANK_DESC == "No Risk" ~ "#FFFFFF",
       COST_RANK_DESC == "Opportunity" ~ 'rgb(31,120,180)',
@@ -109,7 +102,7 @@ proj_risks <- proj_risks %>%
       COST_RANK_DESC == 'High' ~ 'rgb(227,26,28)'
     )
   ) |>
-  mutate(
+  dplyr::mutate(
     'schedulecolor' = case_when(
       SCHEDULE_RANK_DESC == "No Risk" ~ "#FFFFFF",
       SCHEDULE_RANK_DESC == "Opportunity" ~ 'rgb(31,120,180)',
@@ -118,7 +111,7 @@ proj_risks <- proj_risks %>%
       SCHEDULE_RANK_DESC == 'High' ~ 'rgb(227,26,28)'
     )
   ) |>
-  mutate(
+  dplyr::mutate(
     'performancecolor' = case_when(
       PERFORMANCE_RANK_DESC == "No Risk" ~ '#FFFFFF',
       PERFORMANCE_RANK_DESC == "Opportunity" ~ 'rgb(31,120,180)',
@@ -152,12 +145,12 @@ erarr::pie_plots(cost_pie, schedule_pie, perform_pie)
 
 ```{r proj risk log, echo = FALSE, warning=FALSE}
 risk_log_tables <- proj_risks |>
-  select(RISK_IDENTIFIER, RISK_NAME, COST_RISK_RANKING, SCHEDULE_RISK_RANKING, 
+  dplyr::select(RISK_IDENTIFIER, RISK_NAME, COST_RISK_RANKING, SCHEDULE_RISK_RANKING, 
          PERFORMANCEIMPACT_RISK_RANKING, costcolor, schedulecolor, 
          performancecolor)
 
 risk_log_tables |>
-  mutate(
+  dplyr::mutate(
     COST_RISK_RANKING = cell_spec(COST_RISK_RANKING, 
                                   color = costcolor, 
                                   align = 'c', 
@@ -171,11 +164,11 @@ risk_log_tables |>
                                                align = 'c', 
                                                background = performancecolor) 
     ) |>
-  select(RISK_IDENTIFIER, RISK_NAME,COST_RISK_RANKING, SCHEDULE_RISK_RANKING, 
+  dplyr::select(RISK_IDENTIFIER, RISK_NAME,COST_RISK_RANKING, SCHEDULE_RISK_RANKING, 
          PERFORMANCEIMPACT_RISK_RANKING) |>
-  separate(RISK_IDENTIFIER, c("code", "rnkorder"), sep = "-", remove = FALSE) |>
-  arrange(code, as.numeric(rnkorder)) |>
-  select(RISK_IDENTIFIER, RISK_NAME, COST_RISK_RANKING, SCHEDULE_RISK_RANKING, 
+  tidyr::separate(RISK_IDENTIFIER, c("code", "rnkorder"), sep = "-", remove = FALSE) |>
+  dplyr::arrange(code, as.numeric(rnkorder)) |>
+  dplyr::select(RISK_IDENTIFIER, RISK_NAME, COST_RISK_RANKING, SCHEDULE_RISK_RANKING, 
          PERFORMANCEIMPACT_RISK_RANKING) |>
   kbl(format = "html", 
       escape = F, 

diff --git a/inst/app/rmd/ProjectTop4s.Rmd b/inst/app/rmd/ProjectTop4s.Rmd
@@ -3,8 +3,8 @@ title: ""
 runtime: shiny
 output: html_document
 params:
-  projID: ""
-  p2ID: 479265
+  projID: Lee County Conservation Board CAP Sec 204
+  p2ID: ""
   p2sub: ""
 ---
 
@@ -65,12 +65,12 @@ Risk_List_Proj <- RiskDeets
 # Apply filters based on available parameters
 if (params$projID != "") {
   proj_risks <- dplyr::filter(Risk_List_Proj, PROJECT_NAME == params$projID)
-  header <- paste("Project:", Risk_List_Proj$PROJECT_NAME[1])
+  header <- paste("Project:", params$projID)
 }
 
 if (params$p2ID != "") {
   proj_risks<- dplyr::filter(Risk_List_Proj, P2_NUMBER == params$p2ID)
-  header <- paste("P2 Number:", Risk_List_Proj$P2_NUMBER[1])
+  header <- paste("P2 Number:", params$p2ID)
 }
 
 if (params$p2sub != "") {
@@ -85,7 +85,7 @@ header2 <- if (params$p2sub != "") {
   ""
 }
 
-proj_risk_item<- dplyr::slice_head(Risk_List_Proj)
+proj_risk_item<- dplyr::slice_head(proj_risks)
 ```
 
 ###### Report Created On: `r format(Sys.time(), '%d %B, %Y')`
@@ -113,11 +113,11 @@ cat("###",header,header2)
 #### Top 4 Cost Impacts (All Phases)
 ``` {r cost risk log, echo = FALSE, warning=FALSE}
 cost_top4s<-proj_risks |>
-  mutate(MAX_COST = pmax(COST_IMPACT_LOWEST, COST_MEAN, COST_IMPACT_HIGHEST))|>
-  arrange(desc(COST_RISK_RANKING), desc(MAX_COST), desc(PROB_OCCURRENCE))|>
+  dplyr::mutate(MAX_COST = pmax(COST_IMPACT_LOWEST, COST_MEAN, COST_IMPACT_HIGHEST))|>
+  dplyr::arrange(desc(COST_RISK_RANKING), desc(MAX_COST), desc(PROB_OCCURRENCE))|>
       dplyr::select(RISK_IDENTIFIER, RISK_NAME, RISKCATEGORY , MILESTONE , LIKELIHOOD, MAX_COST) |>
     dplyr::slice_head(n=4)|>
-  mutate(MAX_COST = as.character(formattable::currency(MAX_COST)))|>
+  dplyr::mutate(MAX_COST = as.character(formattable::currency(MAX_COST)))|>
   kableExtra::kbl(format = "html", escape = F, col.names =c("Risk ID","Risk Name","Risk Category","Project Milestone","Likelihood", "Mean Cost Impact"), align="clcccc", row.names = FALSE)|>
   kableExtra::kable_styling(bootstrap_options = c( "hover", "condensed", "responsive"))
 
@@ -127,8 +127,8 @@ cost_top4s
 #### Top 4 Schedule Impacts (All Phases)
 ``` {r schedule risk log, echo = FALSE, warning=FALSE}
 schedule_top4s<-proj_risks |>
-   mutate(MAX_SCHED = pmax(SCHEDULE_IMPACT_LOWEST, SCHEDULE_MEAN, SCHEDULE_IMPACT_HIGHEST))|>
-  arrange(desc(SCHEDULE_RISK_RANKING), desc(MAX_SCHED), desc(PROB_OCCURRENCE))|>
+   dplyr::mutate(MAX_SCHED = pmax(SCHEDULE_IMPACT_LOWEST, SCHEDULE_MEAN, SCHEDULE_IMPACT_HIGHEST))|>
+  dplyr::arrange(desc(SCHEDULE_RISK_RANKING), desc(MAX_SCHED), desc(PROB_OCCURRENCE))|>
       dplyr::select(RISK_IDENTIFIER, RISK_NAME, RISKCATEGORY , MILESTONE , LIKELIHOOD, MAX_SCHED) |>
     dplyr::slice_head(n=4)|>
   kableExtra::kbl(format = "html", escape = F, col.names =c("Risk ID","Risk Name","Risk Category","Project Milestone","Likelihood", "Mean Schedule Impact (Days)"), align="clcccc", row.names = FALSE)|>
@@ -141,7 +141,7 @@ schedule_top4s
 #### Top 4 Performance Impacts (All Phases)
 ``` {r perform risk log, echo = FALSE, warning=FALSE}
 perform_log_table<-proj_risks |>
-  arrange(desc(PERFORMANCEIMPACT_RISK_RANKING), desc(PERFORMANCEIMPACT_IMPCT), desc(PROB_OCCURRENCE))|>
+  dplyr::arrange(desc(PERFORMANCEIMPACT_RISK_RANKING), desc(PERFORMANCEIMPACT_IMPCT), desc(PROB_OCCURRENCE))|>
   dplyr::select(RISK_IDENTIFIER, RISK_NAME, RISKCATEGORY , MILESTONE , LIKELIHOOD, PERFORMANCE_RANK_DESC) |>
   dplyr::slice_head(n=4)|>
   kableExtra::kbl(format = "html", escape = F, col.names =c("Risk ID","Risk Name","Risk Category","Project Milestone","Likelihood", "Performance Impact"), align="clcccc", row.names = FALSE)|>