gforge
commented
4 years ago Thanks for the report. I've checked and it seems that you have empty strings for missing values. These should be NA, I've updated the error message in the develop branch so you can see what row and what element is causing the issue:
On row 2 the print of the estimate failed: The estimate '' does not convert into a valid numeric value using grid::convertX
Use NA instead of "" - also the values should be numeric from the onset and not characters.
Dear Max Gordon,
I regularly use your package, which I find very practical and sometimes more flexible than others. Thank you for its development !
Recently, I've been experiencing difficulties to produce a foresplot and I don't know what could be the reason for this. Could you tell me if this is due to a misuse of your package.
Below are the parameters of my session. I also attach a capture of the resulting graph, the script and the data extract used.
script*
db <- structure(list(varname = c("Restriction de participation", " Hommes", " Femmes", "Temps d'activité réduit", " Hommes", " Femmes", "Faible niveau d'éducation", " Hommes", " Femmes", "Sans emploi", " Hommes", " Femmes", "Ménage pauvre", " Hommes", " Femmes", "Confiage dans l'enfance", " Hommes", " Femmes", "Faible soutien social", " Hommes", " Femmes", " "), coef = c("", "1.13", "0.96", "", "3.22", "0.85", "", "1.72", "0.99", "", "-0.84", "-0.25", "", "0.65", "0.54", "", "-0.02", "0.19", "", "0.75", "0.76", ""), ci.low = c("", "0.728", "0.575", "", "2.31", "0.434", "", "1.296", "0.601", "", "-1.401", "-0.78", "", "0.195", "0.085", "", "-0.446", "-0.206", "", "0.298", "0.355", ""), ci.high = c("", "1.535", "1.36", "", "4.432", "1.271", "", "2.164", "1.392", "", "-0.293", "0.272", "", "1.116", "1.001", "", "0.399", "0.582", "", "1.213", "1.18", ""), pval = c("", "<0.001", "<0.001", "", "<0.001", "<0.001", "", "<0.001", "<0.001", "", "0.003", "0.348", "", "0.006", "0.021", "", "0.913", "0.352", "", "0.001", "<0.001", ""), nlab.ph = c("", "123 (59)", "134 (63)", "", "68 (33)", "93 (44)", "", "126 (61)", "120 (57)", "", "163 (78)", "171 (81)", "", "63 (30)", "60 (28)", "", "61 (29)", "85 (40)", "", "67 (32)", "91 (43)", ""), nlab.pt = c("", "67 (32)", "84 (40)", "", "4 (2)", "55 (26)", "", "45 (22)", "69 (33)", "", "184 (88)", "178 (84)", "", "39 (19)", "40 (19)", "", "62 (30)", "76 (36)", "", "39 (19)", "55 (26)", ""), status.lab = c("Personnes handicapées (PH) vs Personnes non handicapées (PnH)", "Personnes handicapées (PH) vs Personnes non handicapées (PnH)", "Personnes handicapées (PH) vs Personnes non handicapées (PnH)", "Personnes handicapées (PH) vs Personnes non handicapées (PnH)", "Personnes handicapées (PH) vs Personnes non handicapées (PnH)", "Personnes handicapées (PH) vs Personnes non handicapées (PnH)", "Personnes handicapées (PH) vs Personnes non handicapées (PnH)", "Personnes handicapées (PH) vs Personnes non handicapées (PnH)", "Personnes handicapées (PH) vs Personnes non handicapées (PnH)", "Personnes handicapées (PH) vs Personnes non handicapées (PnH)", "Personnes handicapées (PH) vs Personnes non handicapées (PnH)", "Personnes handicapées (PH) vs Personnes non handicapées (PnH)", "Personnes handicapées (PH) vs Personnes non handicapées (PnH)", "Personnes handicapées (PH) vs Personnes non handicapées (PnH)", "Personnes handicapées (PH) vs Personnes non handicapées (PnH)", "Personnes handicapées (PH) vs Personnes non handicapées (PnH)", "Personnes handicapées (PH) vs Personnes non handicapées (PnH)", "Personnes handicapées (PH) vs Personnes non handicapées (PnH)", "Personnes handicapées (PH) vs Personnes non handicapées (PnH)", "Personnes handicapées (PH) vs Personnes non handicapées (PnH)", "Personnes handicapées (PH) vs Personnes non handicapées (PnH)", "Personnes handicapées (PH) vs Personnes non handicapées (PnH)" ), coef.lab = c("", "1.13[0.728;1.535]", "0.96[0.575;1.36]", "", "3.22[2.31;4.432]", "0.85[0.434;1.271]", "", "1.72[1.296;2.164]", "0.99[0.601;1.392]", "", "-0.84[-1.401;-0.293]", "-0.25[-0.78;0.272]", "", "0.65[0.195;1.116]", "0.54[0.085;1.001]", "", "-0.02[-0.446;0.399]", "0.19[-0.206;0.582]", "", "0.75[0.298;1.213]", "0.76[0.355;1.18]", "")), row.names = c(NA, -22L), class = c("tbl_df", "tbl", "data.frame" ))
table.text <- cbind( c("Caracteristique",db$varname), c("PH (%)",db$nlab.ph), c("PnH (%)",db$nlab.pt), c("Coef",db$coef), c("p-value",db$pval) )
forestplot(labeltext=table.text, title="PH vs PnH", fn.ci_norm = c(fpDrawNormalCI,#Entete fpDrawNormalCI,fpDrawCircleCI,fpDrawNormalCI, #Restriction de participation fpDrawNormalCI,fpDrawCircleCI,fpDrawNormalCI, #Temps d'activité réduit fpDrawNormalCI,fpDrawNormalCI,fpDrawCircleCI, #Faible niveau d'éducation fpDrawNormalCI,fpDrawCircleCI,fpDrawNormalCI, #Sans emploi fpDrawNormalCI,fpDrawCircleCI,fpDrawNormalCI, #Ménage pauvre fpDrawNormalCI,fpDrawCircleCI,fpDrawNormalCI, #Confiage dans l'enfance fpDrawNormalCI,fpDrawCircleCI,fpDrawNormalCI, #Faible soutien social fpDrawNormalCI), #Pieds de page xlab="Coefficient adjusté sur le groupe d'âge (Coef)", graph.pos = ncol(table.text), mean=c(NA,db$coef), lower=c(NA,db$ci.low), upper=c(NA,db$ci.high), is.summary = c(TRUE,rep(FALSE,nrow(table.text)-2),TRUE), hrzl_lines=list("2"=gpar(lty=1,lwd=2), "23"=gpar(lty=2,lwd=1,columns=c(1:(ncol(table.text)-1),ncol(table.text)+1))), zero=0,line.margin = .1,cex=0.9,lwd.ci=2,boxsize = .25, ci.vertices = TRUE, colgap=unit(3,"mm"), clip=c(-2,5),xticks = c(-2,-1.5,-1,-0.5,0,0.5,1,1.5,2,2.5,3,3.5,4,4.5,5), grid=gpar(lty=3,lwd=1,col="gray75"), txt_gp=fpTxtGp(label = gpar(cex=0.75),ticks=gpar(cex=0.5),xlab = gpar(cex=0.6,fontface="bold")), summary=list("1"=list(gpar(cex=0.7,fontface="bold"),gpar(cex=0.7,fontface="bold"), gpar(cex=0.7,fontface="bold"),gpar(cex=0.7,fontface="bold"), gpar(cex=0.65,fontface="bold")), "23"=list(gpar(cex=0.5,fontface="italic"),gpar(cex=0.5,fontface="italic"), gpar(cex=0.5,fontface="italic"),gpar(cex=0.5,fontface="italic"), gpar(cex=0.5,fontface="italic"))), col=fpColors(box="black", lines="black", zero = "gray25",summary="black") )
Info session
R version 3.5.3 (2019-03-11) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS 10.15.3
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages: [1] grid stats graphics grDevices utils datasets methods base
other attached packages: [1] forcats_0.4.0 stringr_1.4.0 dplyr_0.8.4 purrr_0.3.3 readr_1.3.1 tidyr_1.0.2
[7] tibble_2.1.3 tidyverse_1.3.0 ggplot2_3.2.1 ggpubr_0.2.4 finalfit_0.9.7 forestplot_1.9 [13] FactoMineR_2.0 checkmate_2.0.0 texreg_1.36.23 magrittr_1.5
loaded via a namespace (and not attached): [1] httr_1.4.1 jsonlite_1.6.1 splines_3.5.3 modelr_0.1.5 rmeta_3.0
[6] Formula_1.2-3 assertthat_0.2.1 latticeExtra_0.6-28 cellranger_1.1.0 ggrepel_0.8.1
[11] pillar_1.4.3 backports_1.1.5 lattice_0.20-38 glue_1.3.1 digest_0.6.25
[16] RColorBrewer_1.1-2 ggsignif_0.6.0 rvest_0.3.5 minqa_1.2.4 colorspace_1.4-1
[21] htmltools_0.4.0 Matrix_1.2-18 pkgconfig_2.0.3 broom_0.5.4 haven_2.2.0
[26] scales_1.1.0 dummies_1.5.6 lme4_1.1-21 htmlTable_1.13.3 generics_0.0.2
[31] withr_2.1.2 pan_1.6 nnet_7.3-12 lazyeval_0.2.2 cli_2.0.1
[36] readxl_1.3.1 survival_3.1-8 crayon_1.3.4 mitml_0.3-7 mice_3.7.0
[41] fansi_0.4.1 fs_1.3.1 nlme_3.1-143 MASS_7.3-51.4 xml2_1.2.2
[46] foreign_0.8-72 tools_3.5.3 data.table_1.12.8 hms_0.5.3 lifecycle_0.1.0
[51] reprex_0.3.0 munsell_0.5.0 cluster_2.1.0 packrat_0.5.0 flashClust_1.01-2
[56] compiler_3.5.3 rlang_0.4.4 nloptr_1.2.1 rstudioapi_0.11 htmlwidgets_1.5.1
[61] leaps_3.1 base64enc_0.1-3 boot_1.3-23 gtable_0.3.0 DBI_1.0.0
[66] R6_2.4.1 lubridate_1.7.4 gridExtra_2.3 knitr_1.26 Hmisc_4.3-0
[71] jomo_2.6-10 stringi_1.4.6 parallel_3.5.3 Rcpp_1.0.3 vctrs_0.2.3
[76] rpart_4.1-15 acepack_1.4.1 scatterplot3d_0.3-41 dbplyr_1.4.2 tidyselect_1.0.0
[81] xfun_0.11