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cmmr/rbiom/Issues

bdiv_corrplot calculation method is not using emmeans

#33Closedscilexenko 创建于 2025-11-17
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scilexenkocommented
Hello, I used `bdiv_corrplot` to visualise the corplot and calculate the regression using `emmeans`. For that, I used the following code : ``` a3 <- bdiv_corrplot( biom = biom, #biomclr # healthy controls from Bangladesh and Kenya x = "SoilHumidity", # x-axis variable stat.by = "ZoneCompart", # statistical groups within = c("Compartiment","SamplingZone","Date"), facet.by = c("Date","Compartiment"), fit = "gam", # smoothed trendline trans = "rank", # rank-transform the abundances <==== layers = "tcrp", test = "emmeans", bdiv = "bray", weighted = T, check = TRUE ) ``` However, when I checked the statistics, using `a3$stats`, I got the the following output ``` a3$stats # Model: gam(.distance ~ s(SoilHumidity, by = ZoneCompart, bs = "cs") + ZoneCompart, method = "REML") # A tibble: 9 × 17 SoilHumidity Date Compartiment ZoneCompart .mean.diff .h1 .p.val .adj.p .effect.size .se .n .df .t.ratio .adj.r .aic .bic .loglik <dbl> <fct> <fct> <fct> <dbl> <fct> <dbl> <dbl> <dbl> <dbl> <int> <int> <dbl> <dbl> <dbl> <dbl> <dbl> 1 17.6 27/04/2023 RH ND_RH - AD_RH 113. != 0 1.66e-6 1.49e-5 1.19 22.0 90 86 5.14 2.56e-1 1080. 1091. -536. 2 1.6 06/07/2022 RT ND_RT - AD_RT -266. != 0 3.57e-6 1.61e-5 -3.20 43.0 25 21 -6.20 6.43e-1 298. 305. -144. 3 .................... ``` Here, we see that the model is `gam`, and not `emmeans`. Am I correct ? Can you clarify on this please ? Thank you, Ivan
关闭于 2025-11-17 1 条评论