From 29992c9487a39e9e3a6efd613fcb015c131fcd5b Mon Sep 17 00:00:00 2001 From: sangeetabhatia03 Date: Mon, 19 Aug 2024 17:35:30 +0100 Subject: [PATCH] Use %in% to compare strings to gracefully deal with NAs --- DESCRIPTION | 2 +- NEWS.md | 4 ++ R/filter_df_for_metamean.R | 10 ++--- tests/testthat/test-filter_df_for_metamean.R | 8 ++++ tests/testthat/testdata/offending_dataset.csv | 40 +++++++++++++++++++ 5 files changed, 58 insertions(+), 6 deletions(-) create mode 100644 tests/testthat/testdata/offending_dataset.csv diff --git a/DESCRIPTION b/DESCRIPTION index 770c529..d776f76 100644 --- 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: 1.3.4 +Version: 1.3.5 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 index e5709b7..89f5bd9 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# epireview 1.3.5 + +* BUG-FIX: Fixes #117. NA rows were being created because filter_df_for_metamean used == to compare strings, leading to NAs being created when the RHS was NA. Comparison now is being done using %in%. + # epireview 1.3.4 * DATA: Adds SARS-CoV-1 data (articles, models, and parameters). Outbreaks were not extracted. diff --git a/R/filter_df_for_metamean.R b/R/filter_df_for_metamean.R index a5e4436..9075982 100644 --- a/R/filter_df_for_metamean.R +++ b/R/filter_df_for_metamean.R @@ -43,21 +43,21 @@ filter_df_for_metamean <- function(df) { df <- df[!is.na(df[["population_sample_size"]]), ] df <- df[!is.na(df[["parameter_value"]]), ] - df <- df[df[["parameter_value_type"]] == 'Mean' & + df <- df[df[["parameter_value_type"]] %in% 'Mean' & grepl(x = tolower(df[["parameter_uncertainty_singe_type"]]), pattern = 'standard deviation') | - df[["parameter_value_type"]] == 'Median' & + df[["parameter_value_type"]] %in% 'Median' & grepl(x = tolower(df[["parameter_uncertainty_type"]]), pattern = 'iqr') | - df[["parameter_value_type"]] == 'Median' & + df[["parameter_value_type"]] %in% 'Median' & grepl(x = tolower(df[["parameter_uncertainty_type"]]), pattern = 'range'), ] df$xbar <- ifelse( - df[["parameter_value_type"]] == "Mean", df[["parameter_value"]], NA + df[["parameter_value_type"]] %in% "Mean", df[["parameter_value"]], NA ) df$median <- ifelse( - df[["parameter_value_type"]] == "Median", df[["parameter_value"]], NA + df[["parameter_value_type"]] %in% "Median", df[["parameter_value"]], NA ) df$q1 <- ifelse( grepl(x = tolower(df[["parameter_uncertainty_type"]]), "iqr"), diff --git a/tests/testthat/test-filter_df_for_metamean.R b/tests/testthat/test-filter_df_for_metamean.R index 1c8c210..9547c3a 100644 --- a/tests/testthat/test-filter_df_for_metamean.R +++ b/tests/testthat/test-filter_df_for_metamean.R @@ -50,4 +50,12 @@ test_that("filtering parameter dataframe for meta mean works",{ expect_true(all(!is.na(out$population_sample_size))) expect_true(all(!is.na(out$parameter_value))) expect_true(all(!is.na(out$parameter_unit))) + + ## This dataset should have 17 rows after it is filtered through + ## filter_df_for_metamean + x <- test_path("testdata", "offending_dataset.csv") + df <- read_csv(x, show_col_types = FALSE) + out <- filter_df_for_metamean(df) + expect_equal(dim(out)[1], 17L) + expect_true(all(!is.na(out$id))) }) diff --git a/tests/testthat/testdata/offending_dataset.csv b/tests/testthat/testdata/offending_dataset.csv new file mode 100644 index 0000000..7731bae --- /dev/null +++ b/tests/testthat/testdata/offending_dataset.csv @@ -0,0 +1,40 @@ +id,parameter_data_id,covidence_id,pathogen,parameter_type,parameter_value,exponent,parameter_unit,parameter_lower_bound,parameter_upper_bound,parameter_value_type,parameter_uncertainty_single_value,parameter_uncertainty_singe_type,parameter_uncertainty_lower_value,parameter_uncertainty_upper_value,parameter_uncertainty_type,cfr_ifr_numerator,cfr_ifr_denominator,distribution_type,distribution_par1_value,distribution_par1_type,distribution_par1_uncertainty,distribution_par2_value,distribution_par2_type,distribution_par2_uncertainty,method_from_supplement,method_moment_value,cfr_ifr_method,method_r,method_disaggregated_by,method_disaggregated,method_disaggregated_only,riskfactor_outcome,riskfactor_name,riskfactor_occupation,riskfactor_significant,riskfactor_adjusted,population_sex,population_sample_type,population_group,population_age_min,population_age_max,population_sample_size,population_country,population_location,population_study_start_day,population_study_start_month,population_study_start_year,population_study_end_day,population_study_end_month,population_study_end_year,genome_site,genomic_sequence_available,other_delay_start,other_delay_end,inverse_param,parameter_from_figure,r_pathway,parameter_class,parameter_bounds,comb_uncertainty_type,comb_uncertainty,refs,central,qa_score,article_label +5e0a796c5e859112822487d9d3977029,1f0b9a75bffaeb4ec59c484c30283173,461,SARS-CoV,Human delay - incubation period,5.9,0,Days,1,20,Mean,3.5,Standard Deviation,2.4000000000000004,9.4,NA,NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,Unspecified,NA,NA,NA,FALSE,FALSE,NA,NA,NA,NA,NA,Both,Hospital based,Mixed groups,NA,NA,96,China,Guangzhou,30,Jan-01,2003,10,Mar-03,2003,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,1 - 20,Standard Deviation,3.5,Wu (2003),5.9,0.6,Wu (2003) +d3709e29fa303499c66e0ce9b12035ab,bc402a888c50d456ccef372672e6c6fa,745,SARS-CoV,Human delay - incubation period,3.7,0,Days,NA,NA,Mean,NA,NA,2.6,5.8,95% CrI,NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,NA,NA,NA,Other,TRUE,FALSE,NA,NA,NA,NA,NA,Both,Hospital based,Mixed groups,NA,NA,302,"Hong Kong SAR, China",NA,NA,Feb-02,2003,NA,Jul-07,2003,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,NA,95% CrI,2.6 - 5.8,Virlogeux (2015),3.7,0.8571428571428571,Virlogeux (2015).2 +d3709e29fa303499c66e0ce9b12035ab,4cd65b7e4b66bb8078926e4dbfa8fe6b,745,SARS-CoV,Human delay - incubation period,4.8,0,Days,NA,NA,Mean,NA,NA,4.2,5.5,95% CrI,NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,NA,NA,NA,Other,TRUE,FALSE,NA,NA,NA,NA,NA,Both,Hospital based,Mixed groups,NA,NA,1453,"Hong Kong SAR, China",NA,NA,Feb-02,2003,NA,Jul-07,2003,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,NA,95% CrI,4.2 - 5.5,Virlogeux (2015),4.8,0.8571428571428571,Virlogeux (2015).3 +d3709e29fa303499c66e0ce9b12035ab,db2f9b1ab6da5307849fddeaeb48dc19,745,SARS-CoV,Human delay - incubation period,4.7,0,Days,NA,NA,Mean,NA,NA,4.1,5.4,95% CrI,NA,NA,Normal-Log,NA,NA,FALSE,NA,NA,FALSE,FALSE,NA,NA,NA,Other,TRUE,FALSE,NA,NA,NA,NA,NA,Both,Hospital based,Persons under investigation,NA,NA,234,"Hong Kong SAR, China",NA,NA,Feb-02,2003,NA,Jul-07,2003,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,NA,95% CrI,4.1 - 5.4,Virlogeux (2015),4.7,0.8571428571428571,Virlogeux (2015).4 +d3709e29fa303499c66e0ce9b12035ab,c083f99fe4874217064179e437946bec,745,SARS-CoV,Human delay - incubation period,4.6,0,Days,NA,NA,Standard Deviation,NA,NA,3.6,6,95% CrI,NA,NA,Normal-Log,NA,NA,FALSE,NA,NA,FALSE,FALSE,NA,NA,NA,Other,TRUE,FALSE,NA,NA,NA,NA,NA,Both,Hospital based,Persons under investigation,NA,NA,234,"Hong Kong SAR, China",NA,NA,Feb-02,2003,NA,Jul-07,2003,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,NA,95% CrI,3.6 - 6,Virlogeux (2015),4.6,0.8571428571428571,Virlogeux (2015).5 +02d3210b2ac3cef67e234b2c1e5d98d1,b7bd18e4959e6da66edbb0eb0eb475c2,804,SARS-CoV,Human delay - incubation period,5,0,Days,NA,NA,Mean,NA,NA,2,10,Range,NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,Unspecified,NA,NA,NA,FALSE,FALSE,NA,NA,NA,NA,NA,Unspecified,Hospital based,Persons under investigation,NA,NA,42,Canada,Toronto,14,Mar-03,2003,15,Apr-04,2003,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,NA,Range,2 - 10,Varia (2003),5,0.5714285714285714,Varia (2003) +02d3210b2ac3cef67e234b2c1e5d98d1,e2a49fe3fbcb3431784dd546930dfa4f,804,SARS-CoV,Human delay - incubation period,4,0,Days,NA,NA,Median,NA,NA,2,10,Range,NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,Unspecified,NA,NA,NA,FALSE,FALSE,NA,NA,NA,NA,NA,Unspecified,Hospital based,Persons under investigation,NA,NA,42,Canada,Toronto,14,Mar-03,2003,15,Apr-04,2003,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,NA,Range,2 - 10,Varia (2003),4,0.5714285714285714,Varia (2003).2 +32988e75841cad1ed66434546ccd8737,d7675da4334f21b4b7d4254173bc66f2,1183,SARS-CoV,Human delay - incubation period,4.09,0,Days,NA,NA,Mean,9.65,Variance,0,14,Range,NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,Unspecified,NA,NA,NA,FALSE,FALSE,NA,NA,NA,NA,NA,Unspecified,Hospital based,Persons under investigation,NA,NA,16,"Hong Kong SAR, China",Prince of Wales Hospital,NA,NA,2003,NA,NA,2003,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,NA,Range,0 - 14,Tam (2007),4.09,0.5714285714285714,Tam (2007) +d9ed4c566d928e0fca1ce50be01d32a5,aefc74758420f237cbb61ef96afbaf27,1217,SARS-CoV,Human delay - incubation period,4.7,0,Days,NA,NA,Mean,NA,NA,1,12,Range,NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,Mid outbreak,NA,NA,NA,FALSE,FALSE,NA,NA,NA,NA,NA,Unspecified,Population based,General population,NA,NA,59,Canada,Toronto,23,Feb-02,2003,1,Jul-07,2003,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,NA,Range,1 - 12,Svoboda (2004),4.7,0.7142857142857143,Svoboda (2004).5 +3008559a2374c409bed7c54acb51f3ea,cc83f423bcc553a809124c0a2176c0fc,1401,SARS-CoV,Human delay - incubation period,6,0,Days,1,11,Other,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,Unspecified,NA,NA,Other,FALSE,TRUE,NA,NA,NA,NA,NA,Both,Contact based,Persons under investigation,35,72,10,"Hong Kong SAR, China","Queen Mary Hospital, Kwong Wah Hospital, +and Pamela Youde Nethersole Eastern Hospital",22,Feb-02,2003,22,Mar-03,2003,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,1 - 11,NA,NA,Tsang (2003b),6,1,Tsang (2003b) +7358d9c8a36ba553f1afac4081f1f093,2f86f0823b3c4a7c347790f048a46e9a,1530,SARS-CoV,Human delay - incubation period,5.7,0,Days,NA,NA,Mean,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,Unspecified,NA,NA,NA,FALSE,FALSE,NA,Close contact,NA,NA,NA,Unspecified,Hospital based,Persons under investigation,NA,NA,33,China,Beijing,5,Feb-02,2003,4,May-05,2003,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,NA,NA,NA,Shen (2004),5.7,0.5714285714285714,Shen (2004).2 +601acef372033520ff1629056fa0b454,cd1cecb0378101991e687f6a7eea65a6,2099,SARS-CoV,Human delay - incubation period,3,0,Days,NA,NA,Median,NA,NA,2,6,Range,NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,Post outbreak,NA,NA,NA,FALSE,FALSE,NA,NA,NA,NA,NA,Unspecified,Hospital based,Persons under investigation,NA,NA,11,"Hong Kong SAR, China",Prince of Wales Hospital,4,Mar-03,2003,10,Mar-03,2003,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,NA,Range,2 - 6,Wong (2004),3,0.8571428571428571,Wong (2004).4 +bfe2ce1e1e7a8b19cf30ab300000c889,b6b05d0479e172d1a5a9b1ca84490352,2142,SARS-CoV,Human delay - incubation period,5,0,Days,3,8,Median,NA,NA,1,15,Range,NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,Unspecified,NA,NA,NA,FALSE,FALSE,NA,NA,NA,NA,NA,Unspecified,Hospital based,Healthcare workers,NA,NA,7,Canada,Greater Toronto Area,23,Mar-03,2003,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,3 - 8,Range,1 - 15,Scales (2003),5,0.8,Scales (2003).2 +07fb1db807ae1b5fc5136e4f62d8ea3d,6abd6b01bec25178cf145007f2aa5b98,2541,SARS-CoV,Human delay - incubation period,4,0,Days,NA,NA,NA,NA,NA,2,8,Range,NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,NA,NA,NA,NA,FALSE,FALSE,NA,NA,NA,NA,NA,NA,Travel based,Persons under investigation,NA,NA,22,"Hong Kong SAR, China, Taiwan, China","Hong Kong, Taipei",NA,NA,NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,NA,Range,2 - 8,Olsen (2003),4,1,Olsen (2003).3 +dd21a496485ac60f4d1bf510489fd81f,8fb48d117d9e712ec44753c029c5c1bc,2792,SARS-CoV,Human delay - incubation period,5.3,0,Days,NA,NA,Mean,4.5,Standard Deviation,0.7999999999999998,9.8,NA,NA,NA,Gamma,1.4,Shape,FALSE,0.26,Scale,FALSE,FALSE,NA,NA,NA,NA,FALSE,FALSE,NA,NA,NA,NA,NA,Unspecified,Unspecified,Persons under investigation,NA,NA,85,China,Shanxi,NA,Feb 02,2003,NA,May 05,2003,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,NA,Standard Deviation,4.5,McBryde (2006),5.3,0.8571428571428571,McBryde (2006) +279de96815d0a4a1688b5f5903b6f62a,e1e8cd64db598bae24fde907f2e73c19,3329,SARS-CoV,Human delay - incubation period,6,0,Days,NA,NA,Median,NA,NA,1,15,Range [Sample],NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,NA,NA,NA,NA,FALSE,FALSE,NA,NA,NA,NA,NA,Both,Hospital based,Healthcare workers,21,68,98,"Taiwan, China",NA,1,Nov 11,2002,31,Dec 12,2003,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,NA,Range [Sample],1 - 15,Liu (2016),6,0.6,Liu (2016).2 +279de96815d0a4a1688b5f5903b6f62a,95828cfa41ffef175d5a99abea8281e9,3329,SARS-CoV,Human delay - incubation period,5,0,Days,4,6,Mean,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,NA,NA,NA,NA,FALSE,FALSE,NA,NA,NA,NA,NA,Both,Hospital based,Persons under investigation,0,94,249,"Taiwan, China",NA,1,Nov 11,2002,31,Dec 12,2003,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,4 - 6,NA,NA,Liu (2016),5,0.6,Liu (2016).6 +510b2a9d9062fc2c5232361ae09de710,dcfd3600ac9a8bbc2dda68c7165fb3d6,3478,SARS-CoV,Human delay - incubation period,7.8,0,Days,NA,NA,Mean,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,Mid outbreak,NA,NA,NA,FALSE,FALSE,NA,NA,NA,NA,NA,Unspecified,Hospital based,Persons under investigation,NA,NA,595,China,Beijing,5,Mar 03,2003,20,May 05,2003,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,NA,NA,NA,Liang (2004),7.8,0.6,Liang (2004).2 +4781facdee0e020213c629bfc000d9ba,eaed745f8d0fdbc5db0475fc2b8aef2a,3609,SARS-CoV,Human delay - incubation period,4.83,0,Days,NA,NA,Mean,0.235,Standard Error,4.37,5.29,95% CI,NA,NA,Weibull,5.44,Scale,FALSE,1.91,Shape,FALSE,FALSE,NA,NA,NA,NA,FALSE,FALSE,NA,NA,NA,NA,NA,Unspecified,Mixed settings,Persons under investigation,NA,NA,198,Singapore,NA,NA,Mar 03,2003,NA,Mar 03,2003,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,NA,95% CI,4.37 - 5.29,Kuk (2005),4.83,0.7142857142857143,Kuk (2005) +6bf29469ade5f9302817915c714ccda9,e1282e79b16a1fb76d460e074f482948,3931,SARS-CoV,Human delay - incubation period,4.4,0,Days,NA,NA,Mean,4.6,Standard deviation (Sd) [Sample],-0.1999999999999993,9,NA,NA,NA,Normal-Log,NA,NA,FALSE,NA,NA,FALSE,FALSE,Post outbreak,NA,NA,NA,FALSE,FALSE,NA,NA,NA,NA,NA,Unspecified,Population based,General population,NA,NA,168,"Hong Kong SAR, China",NA,NA,NA,NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,NA,Standard deviation (Sd) [Sample],4.6,Lau (2010),4.4,1,Lau (2010).3 +6bf29469ade5f9302817915c714ccda9,6eac38a52585e2416293aa2cbc4c6b34,3931,SARS-CoV,Human delay - incubation period,5.7,0,Days,NA,NA,Mean,9.7,Standard deviation (Sd) [Sample],-3.999999999999999,15.399999999999999,NA,NA,NA,Normal-Log,NA,NA,FALSE,NA,NA,FALSE,FALSE,Post outbreak,NA,NA,NA,FALSE,FALSE,NA,NA,NA,NA,NA,Unspecified,Population based,General population,NA,NA,97,China,Beijing,NA,NA,NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,NA,Standard deviation (Sd) [Sample],9.7,Lau (2010),5.7,1,Lau (2010).4 +6bf29469ade5f9302817915c714ccda9,6894addaf81aa0983a3a9fc656fbe317,3931,SARS-CoV,Human delay - incubation period,6.9,0,Days,NA,NA,Mean,6.1,Standard deviation (Sd) [Sample],0.8000000000000007,13,NA,NA,NA,Normal-Log,NA,NA,FALSE,NA,NA,FALSE,FALSE,Post outbreak,NA,NA,NA,FALSE,FALSE,NA,NA,NA,NA,NA,Unspecified,Population based,General population,NA,NA,210,"Taiwan, China",NA,NA,NA,NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,NA,Standard deviation (Sd) [Sample],6.1,Lau (2010),6.9,1,Lau (2010).5 +4e761fda72b1e899188a7029b2f79c7c,bfba32f25e6f1023fe835c9d5a904c24,4267,SARS-CoV,Human delay - incubation period,4.6,0,Days,NA,NA,Mean,15.9,Variance,3.8,5.8,95% CI,NA,NA,Gamma,NA,NA,FALSE,NA,NA,FALSE,FALSE,NA,NA,NA,NA,FALSE,FALSE,NA,NA,NA,NA,NA,Unspecified,Unspecified,Persons under investigation,NA,NA,81,"Hong Kong SAR, China",NA,15,Feb 02,2003,31,May 05,2003,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,NA,95% CI,3.8 - 5.8,Leung (2004a),4.6,1,Leung (2004a).1 +cbc89e097372fbb5cdd144cf6b78b364,f01f593386ffbb84bbff759cd4da9495,4334,SARS-CoV,Human delay - incubation period,6,0,Days,NA,NA,Median,NA,NA,2,16,Range [Sample],NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,Mid outbreak,NA,NA,NA,FALSE,FALSE,NA,NA,NA,NA,NA,Both,Hospital based,Persons under investigation,NA,NA,138,"Hong Kong SAR, China",Prince of Wales Hospital,11,Mar 03,2003,25,Mar 03,2003,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,NA,Range [Sample],2 - 16,Lee (2003),6,0.5714285714285714,Lee (2003) +9ba76cb3abe4d299009375c7733b4006,537808fd48273b6fe51c6e3c77736ac2,4455,SARS-CoV,Human delay - incubation period,4,0,Days,NA,NA,Median,NA,NA,2,8,Range [Sample],NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,Start outbreak,NA,NA,NA,FALSE,FALSE,NA,NA,NA,NA,NA,Unspecified,Hospital based,Mixed groups,NA,NA,7,Singapore,Tan Tock Seng Hospital,NA,Feb 02,2003,NA,Mar 03,2003,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,NA,Range [Sample],2 - 8,Hsu (2003),4,0.6666666666666666,Hsu (2003).1 +9ba76cb3abe4d299009375c7733b4006,391d0fb7a1939c38596a1ec67369e7e1,4455,SARS-CoV,Human delay - incubation period,7,0,Days,NA,NA,Median,NA,NA,4,12,Range [Sample],NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,Start outbreak,NA,NA,NA,FALSE,FALSE,NA,NA,NA,NA,NA,Unspecified,Hospital based,Mixed groups,NA,NA,13,Singapore,Tan Tock Seng Hospital,NA,Feb 02,2003,NA,Mar 03,2003,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,NA,Range [Sample],4 - 12,Hsu (2003),7,0.6666666666666666,Hsu (2003).2 +036421829051cf865a1aec10120eea2b,602aa9baa709dc16d60bf76714a903d2,4608,SARS-CoV,Human delay - incubation period,5.1,0,Days,NA,NA,Mean,2.2,Standard Deviation,2.8999999999999995,7.3,NA,NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,NA,NA,NA,NA,FALSE,FALSE,NA,NA,NA,NA,NA,Both,Population based,Persons under investigation,22,84,50,Singapore,NA,25,Feb 02,2003,11,May 05,2003,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,NA,Standard Deviation,2.2,Goh (2006),5.1,1,Goh (2006).1 +036421829051cf865a1aec10120eea2b,79b179ad28f07e63756571aea4e88105,4608,SARS-CoV,Human delay - incubation period,5,0,Days,NA,NA,Median,9,Other,NA,NA,NA,NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,NA,NA,NA,NA,FALSE,FALSE,NA,NA,NA,NA,NA,Both,Population based,Persons under investigation,22,84,50,Singapore,NA,25,Feb 02,2003,11,May 05,2003,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,NA,Other,9,Goh (2006),5,1,Goh (2006).2 +2ba970364602044af074d4dfa0d417ff,c436093149e24356cd62790caed9339d,5282,SARS-CoV,Human delay - incubation period,6.4,0,Days,NA,NA,Mean,NA,NA,5.2,7.7,95% CI,NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,Start outbreak,NA,NA,NA,FALSE,FALSE,NA,NA,NA,NA,NA,Both,Hospital based,General population,NA,NA,1425,"Hong Kong SAR, China",NA,20,Feb 02,2003,28,Apr 04,2003,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,NA,95% CI,5.2 - 7.7,Donnelly (2003),6.4,1,Donnelly (2003) +0c953990453f6236867d02c7493010fc,8d1b59a786b5aad949b069e7d2409248,5393,SARS-CoV,Human delay - incubation period,5.5,0,Days,3,8,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,NA,NA,NA,NA,FALSE,FALSE,NA,NA,NA,NA,NA,Unspecified,Hospital based,Persons under investigation,NA,NA,15,Singapore,Singapore General Hospital,24,Mar 03,2003,15,Apr 04,2003,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,3 - 8,NA,NA,Chow (2004),5.5,0.7142857142857143,Chow (2004) +7a23bf68f9288a3176df31417981e34c,3783e0949262219b24a2f1d6a7fb8805,5512,SARS-CoV,Human delay - incubation period,10.66,0,Days,NA,NA,Other,NA,NA,9.24,13.68,95% CI,NA,NA,log-gamma,NA,NA,FALSE,NA,NA,FALSE,FALSE,NA,NA,NA,NA,FALSE,FALSE,NA,NA,NA,NA,NA,NA,Hospital based,Persons under investigation,NA,NA,128,"Hong Kong SAR, China",NA,NA,NA,NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,NA,95% CI,9.24 - 13.68,Farewell (2005),10.66,1,Farewell (2005) +07aa65bac03197c36ecfb6da7c2444e6,7faf707a2a5f12d6ab286076ecd6f618,5652,SARS-CoV,Human delay - incubation period,10,0,Days,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,Unspecified,NA,NA,NA,FALSE,FALSE,NA,NA,NA,NA,NA,Unspecified,Hospital based,Healthcare workers,NA,NA,45,"Hong Kong SAR, China",Prince of Wales Hospital,NA,Mar 03,2003,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,NA,NA,NA,Cheng (2005b),10,0.8,Cheng (2005b).1 +a98e24fc36ba3d3b8a0af1ec4a57f074,cf5e25bf75081a1d550e9dc17e46e1f6,5758,SARS-CoV,Human delay - incubation period,4,0,Days,NA,NA,Median,NA,NA,3,6,Range [Sample],NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,Unspecified,NA,NA,NA,FALSE,FALSE,NA,NA,NA,NA,NA,Both,Hospital based,Mixed groups,14,82,32,"Taiwan, China",Ho-Ping Hospital,17,Apr 04,2003,26,Apr 04,2003,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,NA,Range [Sample],3 - 6,Chen (2003),4,0.6,Chen (2003) +1f05283044c0e5070e5b7c2a5ff262f1,685aa01d72094b6084454895ca90d130,5878,SARS-CoV,Human delay - incubation period,5.1,0,Days,4.4,5.6,Mean,NA,NA,NA,NA,NA,NA,NA,Normal-Log,5.1,Mean,TRUE,18.3,Variance,TRUE,FALSE,Unspecified,NA,NA,Region,TRUE,FALSE,NA,NA,NA,NA,NA,Both,Population based,Persons under investigation,NA,NA,317,"Canada, Hong Kong SAR, China","Toronto, Hong Kong",NA,NA,NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,4.4 - 5.6,NA,NA,Cowling (2007),5.1,1,Cowling (2007).2 +000c37b67397287f76c05f6eb7bebc8b,3c94d5979f8164063de785819e072e06,6144,SARS-CoV,Human delay - incubation period,5.29,0,Days,2.93,7.17,Mean,12.33,Variance,1.7785900267841126,8.801409973215888,NA,NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,NA,NA,NA,"Age, Occupation, Other, Region, Sex",TRUE,FALSE,NA,NA,NA,NA,NA,Both,Mixed settings,Persons under investigation,NA,NA,209,China,NA,NA,NA,2003,NA,NA,2003,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,2.93 - 7.17,Variance,12.33,Cai (2006),5.29,0.5714285714285714,Cai (2006) +722c038faac20d04eb40d5dbe696ceac,7a94484e1baa0b7154a6d20c7aaaa246,6333,SARS-CoV,Human delay - incubation period,6,0,Days,NA,NA,Median,NA,NA,3,10,IQR,NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,Mid outbreak,NA,NA,NA,FALSE,FALSE,NA,NA,NA,NA,NA,Both,Hospital based,General population,NA,NA,144,Canada,Toronto,7,Mar 03,2003,10,Apr 04,2003,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,NA,IQR,3 - 10,Booth (2003),6,1,Booth (2003) +de7cf97e2ae4f30b0826e6aaafa34a40,0344759b39dcf77c33585727ce9603f7,6607,SARS-CoV,Human delay - incubation period,4,0,Days,NA,NA,Mean,3,Standard deviation (Sd) [Sample],1,7,NA,NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,Mid outbreak,NA,NA,"Age, Sex",TRUE,FALSE,NA,NA,NA,NA,NA,Female,Hospital based,Healthcare workers,38,53,4,Canada,Toronto,23,Mar 03,2003,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,NA,Standard deviation (Sd) [Sample],3,Avendano (2003),4,1,Avendano (2003) +de7cf97e2ae4f30b0826e6aaafa34a40,20cb8683658108a6c2f329b895789750,6607,SARS-CoV,Human delay - incubation period,3.5,0,Days,NA,NA,Mean,3,Standard deviation (Sd) [Sample],0.5,6.5,NA,NA,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,Mid outbreak,NA,NA,"Age, Sex",TRUE,FALSE,NA,NA,NA,NA,NA,Both,Hospital based,Healthcare workers,27,63,10,Canada,Toronto,23,Mar 03,2003,NA,NA,NA,NA,FALSE,NA,NA,FALSE,FALSE,NA,Human delay,NA,Standard deviation (Sd) [Sample],3,Avendano (2003),3.5,1,Avendano (2003).1