mrc-ide · sangeetabhatia03 · Jul 19, 2024 · Jul 11, 2024 · Jul 11, 2024 · Jul 11, 2024
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -4,13 +4,11 @@ on:
   push:
     branches:
       - main
-      - master
+      - develop
   pull_request:
     branches:
       - main
-      - master
-  schedule:
-  - cron: '0 6 * * 1' # Run every Monday at 06:00 (UTC)
+      - develop
 
 name: R-CMD-check
 

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -2,11 +2,13 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master]
+    branches:
+      - main
+      - develop
   pull_request:
-    branches: [main, master]
-  release:
-    types: [published]
+    branches:
+      - main
+      - develop
   workflow_dispatch:
 
 name: pkgdown
@@ -40,7 +42,7 @@ jobs:
         shell: Rscript {0}
 
       - name: Deploy to GitHub pages 🚀
-        if: github.event_name != 'pull_request'
+        if: github.event_name == 'push' && github.ref == 'refs/heads/main'
         uses: JamesIves/github-pages-deploy-action@v4.4.1
         with:
           clean: false

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: epireview
 Title: Tools to update and summarise the latest pathogen data from the Pathogen Epidemiology Review Group (PERG)
-Version: 1.3.0
+Version: 1.3.1
 Authors@R: c(
     person("Rebecca", "Nash", email = "r.nash@imperial.ac.uk", role = "aut",
            comment = c(ORCID = "0000-0002-5213-4364")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,10 @@
 # epireview 1.3.0
 
+* FEATURE
+  - Updated lassa data available following updated literature search
+
+# epireview 1.3.0
+
 * MAJOR RELEASE
   - Improved messages when loading data via load_epidata
   - User-friendly getters for key epi parameters

diff --git a/inst/extdata/lassa_articles.csv b/inst/extdata/lassa_articles.csv
diff --git a/inst/extdata/lassa_models.csv b/inst/extdata/lassa_models.csv
diff --git a/inst/extdata/lassa_outbreaks.csv b/inst/extdata/lassa_outbreaks.csv
@@ -2,28 +2,30 @@ id,outbreak_data_id,covidence_id,pathogen,outbreak_start_day,outbreak_start_mont
 9da04c9c3464ba932aa82d2e4a0fb5ea,00e2733a168ab3ea8f8c9fbb50e9ab1b,60,Lassa mammarenavirus,1,Jan,2018,29,Apr,2018,NA,FALSE,Nigeria,NA,420,Unspecified,NA,NA,NA,106,Endemic equilibrium,FALSE
 b1ed69167fd7c17d124b8f1bf65329e1,8ced256dd0fec2c2fa8c3f1ae5917db7,61,Lassa mammarenavirus,NA,Jan,1970,NA,NA,NA,NA,FALSE,Nigeria,Jos Plateau,13,Unspecified,26,NA,NA,10,Unspecified,TRUE
 39819a2a94765a2302e96fca8c7de0bd,6493a15fce9bb839f999a47e2bc40e48,152,Lassa mammarenavirus,NA,Dec,2017,NA,May,2018,NA,FALSE,Nigeria,NA,431,Molecular (PCR etc),NA,NA,NA,NA,Endemic equilibrium,FALSE
-a7ab005860fa1caba3ba17bae7c7ebb6,6df0780469ebe8a022cb69943ab3151e,558,Lassa mammarenavirus,27,Apr,2010,31,Jan,2012,NA,FALSE,Sierra Leone,Kenema Government Hospital,NA,Unspecified,1002,NA,NA,NA,Unspecified,FALSE
-dc58ccb401238d09a9ba6452086ea3ac,33c744165caeec50bb78b57e020f8299,560,Lassa mammarenavirus,25,Dec,1969,NA,NA,NA,2,FALSE,Nigeria,Jos,23,Unspecified,NA,NA,NA,NA,Endemic equilibrium,FALSE
-dc58ccb401238d09a9ba6452086ea3ac,28f2fb63eda710078594e1861c7af821,560,Lassa mammarenavirus,NA,Mar,1972,NA,Apr,1972,1,FALSE,Liberia,Zorzor,11,Unspecified,NA,NA,NA,NA,Endemic equilibrium,FALSE
-dc58ccb401238d09a9ba6452086ea3ac,645cb2ec17f3fc72ab87a11707da6a10,560,Lassa mammarenavirus,27,Apr,2010,31,Jan,2012,NA,FALSE,Sierra Leone,Kenema Government Hospital,295,Molecular (PCR etc),1002,NA,NA,NA,Endemic equilibrium,FALSE
-efb15bb557943d996a14bbe398aa6b8f,e106ba2475561eba61c5ed701446a239,832,Lassa mammarenavirus,23,Sep,1972,15,Oct,1972,NA,FALSE,Sierra Leone,Panguma; Tongo,12,Molecular (PCR etc),20,NA,NA,NA,Endemic equilibrium,FALSE
-5e7d20c0d0d52495025dc8a09f656096,da5b689447af705b1d6025ccb10982f9,840,Lassa mammarenavirus,NA,Jul,1980,NA,Apr,1982,NA,FALSE,Liberia,Curran Lutheran Hospital; Zorzor,14,Molecular (PCR etc),NA,NA,NA,NA,Unspecified,FALSE
-2e4ff9c8065b9faadd3a386783fc93e3,922befc25f233a98daf50c4d7583db71,842,Lassa mammarenavirus,12,Jan,1969,3,May,1969,NA,FALSE,Nigeria,Lassa; Jos,NA,Unspecified,3,NA,NA,2,Unspecified,FALSE
-8b9eae26603fabaa7c46c0d0880e7035,b1670571dd36918841cc1840fcee35fa,1161,Lassa mammarenavirus,NA,Jan,1970,NA,Feb,1970,NA,FALSE,Nigeria,Jos,15,Molecular (PCR etc),13,NA,NA,13,Unspecified,FALSE
-bd5e179ceac6d7d3a08d2686781dd8c8,de064e4b763fcd33a2bd62c34a338191,1173,Lassa mammarenavirus,1,Dec,2015,30,Apr,2016,NA,FALSE,Nigeria,Ondo State,19,Molecular (PCR etc),NA,NA,NA,12,Endemic equilibrium,FALSE
-ee9a2b7c5f5092606151f83de44d102f,fcd3ff43ea5944e68d14b44aa47f6afa,1183,Lassa mammarenavirus,1,Jan,2017,25,Mar,2017,3,FALSE,Nigeria,NA,107,Unspecified,NA,NA,NA,50,Endemic equilibrium,FALSE
-ee9a2b7c5f5092606151f83de44d102f,eef5e9507eac660e2537865a666476eb,1183,Lassa mammarenavirus,1,Jan,2018,25,Mar,2018,3,FALSE,Nigeria,NA,394,Unspecified,NA,NA,NA,104,Endemic equilibrium,FALSE
-8fdea1afb902a4cfacf42853b8e222e6,f4299d05ee4ccd66d8e7c31791a2f9ba,1254,Lassa mammarenavirus,NA,Jan,2016,NA,Jun,2016,NA,FALSE,Liberia,Bong; Nimba; Montserrado,14,Molecular (PCR etc),14,NA,NA,19,Endemic equilibrium,FALSE
-26839290fc754199f5fb8287714a2689,82e5d95e67ffbf56badee8f6848b2180,1272,Lassa mammarenavirus,NA,Oct,2015,NA,Feb,2016,NA,FALSE,Nigeria,Taraba; Edo; Lagos; Bauchi; Rivers; Gombe; Ekiti,47,Molecular (PCR etc),NA,NA,NA,28,Endemic equilibrium,FALSE
-2c298b19cc69c9ac1aeedf4b8178f350,30cb31c87495d754385310ae1d5f86bf,1310,Lassa mammarenavirus,NA,Jan,1974,NA,Feb,1974,NA,FALSE,Nigeria,Onitsha,3,Molecular (PCR etc),NA,NA,NA,1,Unspecified,FALSE
-d2ecc47171bdd43a29fed1a9e927fe9f,cb001054b9662bf7bfceaff3a036fe4b,1433,Lassa mammarenavirus,NA,Jan,1997,NA,Apr,1997,4,FALSE,Sierra Leone,Kenema ; Kailahun,NA,Molecular (PCR etc),NA,NA,352,NA,Unspecified,FALSE
-f14b287ccc8da2a837c4d9d3ae2b3394,86fefbcfa0e6715e7355fae930c8ccde,1447,Lassa mammarenavirus,1,Jan,2012,25,Mar,2012,NA,FALSE,Nigeria,Ebonyi State,10,Molecular (PCR etc),10,NA,NA,6,Endemic equilibrium,FALSE
-8321fdc6e9cc33f09d4f4c0e58c71c08,83bc94e420b12884eec0036be4caea4f,2589,Lassa mammarenavirus,1,Jan,2018,6,May,2018,4,FALSE,Nigeria,NA,423,Molecular (PCR etc),10,NA,NA,106,Endemic equilibrium,FALSE
-8dcd9631796bbe52a7ae56ac6da2807a,da822d7af7d63b40c2170c835af2988c,2611,Lassa mammarenavirus,30,Oct,2019,16,Nov,2019,1,FALSE,Sierra Leone,Tonkolili District,3,Molecular (PCR etc),2,NA,NA,3,Endemic equilibrium,FALSE
-e2d105ecdca74084b6c652802b2c4516,3d1ae4a5d64202801eb1023880cc84d1,2651,Lassa mammarenavirus,NA,Oct,2014,NA,Nov,2014,1,FALSE,Benin,Northern Benin,2,Molecular (PCR etc),11,NA,NA,11,Unspecified,FALSE
-e2d105ecdca74084b6c652802b2c4516,d38236092243b817083ec27802c43b93,2651,Lassa mammarenavirus,NA,Dec,2015,NA,Mar,2016,3,FALSE,Benin,Borgou; Donga;Collines; Alibori; Plateau; Ouémé; Atlantique; Litoral,18,Molecular (PCR etc),3,NA,NA,11,Unspecified,FALSE
-0917806f0819d3a2318412fdbbe70d4a,102ce34a6e9e768d3841366fca6c9c81,3635,Lassa mammarenavirus,1,Jan,2019,29,Dec,2019,12,FALSE,Nigeria,Edo; Ondo; Ebonyi,833,Molecular (PCR etc),5057,NA,NA,174,Unspecified,FALSE
-a07d714192f45231e3edbb2921a3143c,2dbb85545fc17678fec712387bd9f0a4,3991,Lassa mammarenavirus,NA,NA,2018,NA,NA,2019,NA,FALSE,Nigeria,NA,1463,Molecular (PCR etc),NA,NA,NA,344,Endemic equilibrium,FALSE
-c772c487685dfd7937fbdd62ceb345e2,ecdaa1da15ace6aa3b601483a15d0240,4314,Lassa mammarenavirus,NA,NA,2017,NA,NA,2017,NA,FALSE,Nigeria,NA,312,Unspecified,NA,NA,NA,78,Unspecified,FALSE
-bd7b34286855ff335accb6bdbd83f694,323e39e17fca03ed666f5c0545e987a6,4316,Lassa mammarenavirus,1,Jan,2018,18,Mar,2018,NA,FALSE,Nigeria,Anambra; Bauchi; Benue; Delta; Ebonyi; Edo; Ekiti; Fct; Abuja; Gombe; Imo; Kaduna; Kogi; Lagos; Nasarawa; Ondo; Osun; Plateau; Rivers; Taraba,376,Unspecified,1495,NA,NA,95,Unspecified,FALSE
-b895ff1b44ba2b783c78ba3185fb2c28,5b6b37f17d74f50b2d54e61edb597118,4745,Lassa mammarenavirus,NA,Mar,1972,NA,Apr,1972,NA,FALSE,Liberia,Zorzor,11,Unspecified,NA,NA,NA,4,Unspecified,FALSE
+b893c462fb12cdd6ba814be4fd7ff372,523d78ff0e284e2a6f436ffc479597a9,558,Lassa mammarenavirus,27,Apr,2010,31,Jan,2012,NA,FALSE,Sierra Leone,Kenema Government Hospital,NA,Unspecified,1002,NA,NA,NA,Unspecified,FALSE
+ab5a1f40f53f9afd427cf89da33bfe99,4aba7442d20d4c4e2d86d02fe2e25020,560,Lassa mammarenavirus,25,Dec,1969,NA,NA,NA,2,FALSE,Nigeria,Jos,23,Unspecified,NA,NA,NA,NA,Endemic equilibrium,FALSE
+ab5a1f40f53f9afd427cf89da33bfe99,141e6dd0015dc8e951e9700c2ecb30d1,560,Lassa mammarenavirus,NA,Mar,1972,NA,Apr,1972,1,FALSE,Liberia,Zorzor,11,Unspecified,NA,NA,NA,NA,Endemic equilibrium,FALSE
+ab5a1f40f53f9afd427cf89da33bfe99,f0bf58ffbebdae14853ed59de3f67441,560,Lassa mammarenavirus,27,Apr,2010,31,Jan,2012,NA,FALSE,Sierra Leone,Kenema Government Hospital,295,Molecular (PCR etc),1002,NA,NA,NA,Endemic equilibrium,FALSE
+660f431c3cc58327c010c0cae50c1a86,8b8e78d16bacfe020ac68c299facc3f0,832,Lassa mammarenavirus,23,Sep,1972,15,Oct,1972,NA,FALSE,Sierra Leone,Panguma; Tongo,12,Molecular (PCR etc),20,NA,NA,NA,Endemic equilibrium,FALSE
+f3e0da17630314ea0ff0276cac6aee00,5c7a0e19d5b63ecc2636b9535e5c787c,840,Lassa mammarenavirus,NA,Jul,1980,NA,Apr,1982,NA,FALSE,Liberia,Curran Lutheran Hospital; Zorzor,14,Molecular (PCR etc),NA,NA,NA,NA,Unspecified,FALSE
+bf0fa77e86f391b4b01b755a19c3d17a,3b551a8affff125a32b5dde91d2fdad7,842,Lassa mammarenavirus,12,Jan,1969,3,May,1969,NA,FALSE,Nigeria,Lassa; Jos,NA,Unspecified,3,NA,NA,2,Unspecified,FALSE
+e41ac915202bb0bd4d14559cae049b2b,942121f23ea146378d8f94572be80d6c,1161,Lassa mammarenavirus,NA,Jan,1970,NA,Feb,1970,NA,FALSE,Nigeria,Jos,15,Molecular (PCR etc),13,NA,NA,13,Unspecified,FALSE
+a1a530432af637ad1a77bdc7205db000,9f8b78c822a60ce0c977969286a19ffd,1173,Lassa mammarenavirus,1,Dec,2015,30,Apr,2016,NA,FALSE,Nigeria,Ondo State,19,Molecular (PCR etc),NA,NA,NA,12,Endemic equilibrium,FALSE
+3b03ec9238bd26c47a0733c9da8dd6df,b00b32038b17bda1f879a075a9b98bc0,1183,Lassa mammarenavirus,1,Jan,2017,25,Mar,2017,3,FALSE,Nigeria,NA,107,Unspecified,NA,NA,NA,50,Endemic equilibrium,FALSE
+3b03ec9238bd26c47a0733c9da8dd6df,c06c4ea210bbf509b8514845de76fa7b,1183,Lassa mammarenavirus,1,Jan,2018,25,Mar,2018,3,FALSE,Nigeria,NA,394,Unspecified,NA,NA,NA,104,Endemic equilibrium,FALSE
+cf191c255fcd483b5fde439c73ccba5d,4abbcd9e19b65444ae882cc1232879f5,1254,Lassa mammarenavirus,NA,Jan,2016,NA,Jun,2016,NA,FALSE,Liberia,Bong; Nimba; Montserrado,14,Molecular (PCR etc),14,NA,NA,19,Endemic equilibrium,FALSE
+186ed2567f0202b6d9745058e5dda626,8461cef5a5d4cda56befcc2bd953c8c6,1272,Lassa mammarenavirus,NA,Oct,2015,NA,Feb,2016,NA,FALSE,Nigeria,Taraba; Edo; Lagos; Bauchi; Rivers; Gombe; Ekiti,47,Molecular (PCR etc),NA,NA,NA,28,Endemic equilibrium,FALSE
+6713b50ed8aaef50b892b5854b3c7ca6,39dbf88913f1e3b949184fd358152a31,1310,Lassa mammarenavirus,NA,Jan,1974,NA,Feb,1974,NA,FALSE,Nigeria,Onitsha,3,Molecular (PCR etc),NA,NA,NA,1,Unspecified,FALSE
+d53e41555e6b86e22716dd2e61dea71b,eaa40e06bbe3b4121420c56732cb1781,1433,Lassa mammarenavirus,NA,Jan,1997,NA,Apr,1997,4,FALSE,Sierra Leone,Kenema ; Kailahun,NA,Molecular (PCR etc),NA,NA,352,NA,Unspecified,FALSE
+4c9575bdcf6ae5281801b768a563ac91,270ee9eb9bf28affce33cd0b7e3d25e7,1447,Lassa mammarenavirus,1,Jan,2012,25,Mar,2012,NA,FALSE,Nigeria,Ebonyi State,10,Molecular (PCR etc),10,NA,NA,6,Endemic equilibrium,FALSE
+bfa7e3af198a4dbd6808e8c4aee7d6ce,de5d0a6a4116ccb45626ca934fca2157,2589,Lassa mammarenavirus,1,Jan,2018,6,May,2018,4,FALSE,Nigeria,NA,423,Molecular (PCR etc),10,NA,NA,106,Endemic equilibrium,FALSE
+4a72bcc3746fb9257527302306bffc7c,12f322bd60a5193d5b1bdb4a25e9ab77,2611,Lassa mammarenavirus,30,Oct,2019,16,Nov,2019,1,FALSE,Sierra Leone,Tonkolili District,3,Molecular (PCR etc),2,NA,NA,3,Endemic equilibrium,FALSE
+b6f7bbca62bd7d2ccf131cc6d79bc1b1,8bfdfff55287081ef41e9df1f693a166,2651,Lassa mammarenavirus,NA,Oct,2014,NA,Nov,2014,1,FALSE,Benin,Northern Benin,2,Molecular (PCR etc),11,NA,NA,11,Unspecified,FALSE
+b6f7bbca62bd7d2ccf131cc6d79bc1b1,f1e9a3ba7b834a1e8c6b196eea99d626,2651,Lassa mammarenavirus,NA,Dec,2015,NA,Mar,2016,3,FALSE,Benin,Borgou; Donga;Collines; Alibori; Plateau; Ouémé; Atlantique; Litoral,18,Molecular (PCR etc),3,NA,NA,11,Unspecified,FALSE
+ea5e1757b611b55eaf481e7a9c3ec178,4542610277df6808a35f50dfbb5290b8,2791,Lassa mammarenavirus,1,Jan,2019,28,Apr,2019,NA,FALSE,Nigeria,NA,554,Molecular (PCR etc),2323,NA,NA,124,Endemic equilibrium,TRUE
+0db8faf852447230548f66dda6881c6b,c71904ecf3593ad6e99446967a539114,3635,Lassa mammarenavirus,1,Jan,2019,29,Dec,2019,12,FALSE,Nigeria,Edo; Ondo; Ebonyi,833,Molecular (PCR etc),5057,NA,NA,174,Unspecified,FALSE
+5c5ffbe66a43c846fd20725dd3e4ad45,1592a5d71badba4513bce1dfea74110a,3991,Lassa mammarenavirus,NA,NA,2018,NA,NA,2019,NA,FALSE,Nigeria,NA,1463,Molecular (PCR etc),NA,NA,NA,344,Endemic equilibrium,FALSE
+d7d8fa31fe3fbe2936d94b520ae2bf31,c530701d6c067fe042aab0b4a160b87d,4314,Lassa mammarenavirus,NA,NA,2017,NA,NA,2017,NA,FALSE,Nigeria,NA,312,Unspecified,NA,NA,NA,78,Unspecified,FALSE
+e5a6593dcd8e54d70102ba5381e61da8,f3b73b417d07814f646dc68e827c7d5e,4316,Lassa mammarenavirus,1,Jan,2018,18,Mar,2018,NA,FALSE,Nigeria,Anambra; Bauchi; Benue; Delta; Ebonyi; Edo; Ekiti; Fct; Abuja; Gombe; Imo; Kaduna; Kogi; Lagos; Nasarawa; Ondo; Osun; Plateau; Rivers; Taraba,376,Unspecified,1495,NA,NA,95,Unspecified,FALSE
+23eb68904ae4f092f0f7310d85c13cad,ed3b90ac037d1cc4e815b3d8be0a4df1,4745,Lassa mammarenavirus,NA,Mar,1972,NA,Apr,1972,NA,FALSE,Liberia,Zorzor,11,Unspecified,NA,NA,NA,4,Unspecified,FALSE
+73acbbf9fab54e3c24e4695a9ce1038f,cf9618b10a7c39d81f8ce2fc580aebf6,5623,Lassa mammarenavirus,1,Jan,2018,21,Apr,2018,NA,FALSE,Nigeria,NA,416,Molecular (PCR etc),1865,NA,NA,105,Endemic equilibrium,TRUE