add rhub

timat35 · Sep 18, 2024 · e992e3f · e992e3f
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -2,3 +2,5 @@
 ^README\.Rmd$
 ^NEWS\.Rmd$
 ^README-.*\.png$
+^dev$
+^release$
diff --git a/.github/workflows/rhub.yaml b/.github/workflows/rhub.yaml
@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
diff --git a/dev/ICD_CI5XI.csv b/dev/ICD_CI5XI.csv
@@ -0,0 +1,69 @@
+ICD,LABEL
+C00,Lip
+C01-02,Tongue
+C03-06,Mouth
+C07-08,Salivary glands
+C09,Tonsil
+C10,Other oropharynx
+C11,Nasopharynx
+C12-13,Hypopharynx
+C14,Pharynx unspecified
+C15,Oesophagus
+C16,Stomach
+C17,Small intestine
+C18,Colon
+C19-20,Rectum
+C21,Anus
+C22,Liver
+C23-24,Gallbladder etc.
+C25,Pancreas
+C30-31,"Nose, sinuses etc."
+C32,Larynx
+C33-34,Lung (incl. trachea and bronchus)
+C37-38,Other thoracic organs
+C40-41,Bone
+C43,Melanoma of skin
+C44,Other skin
+C45,Mesothelioma
+C46,Kaposi sarcoma
+"C47,C49",Connective and soft tissue
+C50,Breast
+C51,Vulva
+C52,Vagina
+C53,Cervix uteri
+C54,Corpus uteri
+C55,Uterus unspecified
+C56,Ovary
+C57,Other female genital organs
+C58,Placenta
+C60,Penis
+C61,Prostate
+C62,Testis
+C63,Other male genital organs
+C64,Kidney
+C65,Renal pelvis
+C66,Ureter
+C67,Bladder
+C68,Other urinary organs
+C69,Eye
+C70-72,"Brain, nervous system"
+C73,Thyroid
+C74,Adrenal gland
+C75,Other endocrine
+C81,Hodgkin disease
+"C82-86,C96",Non-Hodgkin lymphoma
+C88,Immunoproliferative diseases
+C90,Multiple myeloma
+C91,Lymphoid leukaemia
+C92-94,Myeloid leukaemia
+C95,Leukaemia unspecified
+C26-29,Other
+C35-36,Other
+C39,Other
+C42,Other
+C48,Other
+C59,Other
+C76-80,Other
+C87,Other
+C89,Other
+C97-99,Other
diff --git a/dev/ICD_globocan.csv b/dev/ICD_globocan.csv
@@ -0,0 +1,43 @@
+ICD,LABEL
+C00-08,"Lip, oral cavity"
+C11,Nasopharynx
+"C09-10,C12-14",Other pharynx
+C15,Oesophagus
+C16,Stomach
+C18-21,Colorectum
+C22,Liver
+C23-24,Gallbladder
+C25,Pancreas
+C32,Larynx
+C33-34,Lung
+C43,Melanoma of skin
+C44,Other skin
+C45,Mesothelioma
+C46,Kaposi sarcoma
+C50,Breast
+C51,Vulva
+C52,Vagina
+C53,Cervix uteri
+C54,Corpus uteri
+C56,Ovary
+C61,Prostate
+C62,Testis
+C64-66,Kidney
+C67,Bladder
+C70-72,"Brain, nervous system"
+C73,Thyroid
+C81,Hodgkin disease
+"C82-86,C96",Non-Hodgkin lymphoma
+"C88,C90",Multiple myeloma
+C91-95,Leukaemia
+C17,Other
+C26-31,Other
+C35-42,Other
+C47-49,Other
+C55,Other
+C57-60,Other
+C63,Other
+C68-69,Other
+C74-80,Other
+C87,Other
+C89,Other
diff --git a/dev/Rcan_example.R b/dev/Rcan_example.R
@@ -0,0 +1,135 @@
+library(Rcan)
+
+data(csu_registry_data_2)
+
+
+# ASR with standard error with missing age.
+df_asr <- csu_asr(csu_registry_data_2, 
+                  "age", "cases", "py",
+                  group_by = c("registry", "registry_label", "sex", "year", "ethnic" ),
+                  var_age_group = c("registry_label"), 
+                  var_st_err = "st_err")
+
+df_asr[1:4,]	
+
+# Truncated ASR, 25-69 years.
+result <- csu_asr(csu_registry_data_2, 
+                  "age", "cases", "py",
+                  group_by = c("registry", "registry_label", "sex", "year", "ethnic" ),
+                  var_age_group = c("registry_label"), 
+                  var_st_err = "st_err",
+                  first_age = 6, 
+                  last_age = 14,
+                  missing_age = 99)	
+
+result[1:4,]	
+
+
+# EAPC with standard error		
+df_eapc <- csu_eapc(df_asr,
+                    "asr", "year",
+                    group_by=c("registry", "registry_label", "sex", "ethnic" ))
+
+df_eapc[1:4,]	
+
+
+
+data(csu_registry_data_1)
+# plot age specific rate for 1 population.
+df_colombia <- csu_registry_data_1[csu_registry_data_1$registry_label=="Colombia, Cali",]
+
+csu_ageSpecific(df_colombia,
+                plot_title = "Colombia, Liver, male")
+
+# plot age specific rate for 1 population, and comparison with CI5XI data.
+csu_ageSpecific(df_colombia,
+                plot_title = "Colombia, Liver, male",
+                CI5_comparison = "Liver")
+
+# plot age specific rate for 4 population, legend at the bottom and comparison with CI5XI data.
+csu_ageSpecific(csu_registry_data_1,
+                group_by="registry_label",
+                logscale = TRUE,
+                legend=csu_trend_legend(position="right", right_space_margin = 6.5),
+                plot_title = "Liver, male")
+
+
+# age specific top 5
+data("csu_CI5X_data")
+
+#remove all cancers:
+df_data <- csu_CI5X_data[csu_CI5X_data$cancer_code < 62,]
+#select Thailand changmai
+df_data_1 <- df_data[df_data$registry_code==76401,]
+#select USAm NPCR
+df_data_2 <- df_data[df_data$registry_code== 84080,]
+
+
+# plot for Thailand Changmai
+dt_result_1 <- csu_ageSpecific_top(df_data_1,
+                                   var_age="age", 
+                                   var_cases="cases", 
+                                   var_py="py",
+                                   var_top="cancer_label", 
+                                   group_by="sex", 
+                                   plot_title= "Thailand, Chiangmai",
+                                   plot_subtitle = "Top 5 cancer",
+                                   missing_age = 19)
+
+
+# plot for USA NPCR
+dt_result_2 <- csu_ageSpecific_top(df_data_2,
+                                   var_age="age", 
+                                   var_cases="cases", 
+                                   var_py="py",
+                                   logscale=TRUE,
+                                   var_top="cancer_label", 
+                                   group_by="sex", 
+                                   plot_title= "USA, NPCR",
+                                   plot_subtitle = "Top 5 cancer",
+                                   missing_age = 19)
+
+
+#cohort period graph
+data(csu_registry_data_2)
+
+# to select only 1 population 
+test <- csu_registry_data_2[csu_registry_data_2$registry == 84020,]
+test <- test[test$sex==1,]
+
+# plot cohort graph from 25-29 years until 75-79 years.
+csu_trendCohortPeriod(df_data=test,
+                      missing_age =99,
+                      plot_title = "USA, Liver, males")
+
+# plot Period graph from 0-5 until 85+.
+csu_trendCohortPeriod(df_data=test,
+                      missing_age =99,
+                      plot_title = "USA, Liver, males",
+                      type="Period",
+                      first_age=1,
+                      last_age=18)
+
+# plot Cohort-Period graph from 30-64 years until 70-74 years.
+csu_trendCohortPeriod(df_data=test,
+                      missing_age =99,
+                      plot_title = "USA, Liver, males",
+                      type="Both",
+                      first_age=7,
+                      last_age=15)
+
+# plot Cohort-Period graph from 30-64 years until 70-74 years with Y axis normal scale.
+csu_trendCohortPeriod(df_data=test,
+                      missing_age =99,
+                      plot_title = "USA, Liver, males",
+                      type="Both",
+                      first_age=7,
+                      last_age=15,
+                      logscale=FALSE)
+
+# plot Cohort graph from 25-29 years until 75-79 years, with data grouped in 2 years period.
+csu_trendCohortPeriod(df_data=test,
+                      missing_age =99,
+                      plot_title = "USA, Liver, males",
+                      type="Cohort",
+                      year_group = 2)