Clean workflow

Remove results file with dot as name separator
Cleaned data is now saved in data/cleaned/

results/raw/2.various_stats.txt

-[1] "anova table:"
-Analysis of Variance Table
-
-Response: yield
-           Df  Sum Sq Mean Sq  F value Pr(>F)    
-farm        2   0.279   0.139   0.2634 0.7691    
-fertilizer  2 259.292 129.646 245.1385 <2e-16 ***
-Residuals  81  42.838   0.529                    
----
-Signif. codes:  0 *** 0.001 ** 0.01 * 0.05 . 0.1   1
-[1] "em means table:"
- farm        fertilizer  emmean    SE df lower.CL upper.CL
- de Jong     Efficientie  12.93 0.173 81    12.59    13.28
- de Kerk     Efficientie  13.05 0.173 81    12.70    13.39
- van de Boer Efficientie  13.15 0.178 81    12.80    13.50
- de Jong     Miracle      10.51 0.173 81    10.16    10.85
- de Kerk     Miracle      10.62 0.177 81    10.27    10.97
- van de Boer Miracle      10.72 0.174 81    10.38    11.07
- de Jong     SuperDash     8.69 0.178 81     8.33     9.04
- de Kerk     SuperDash     8.80 0.174 81     8.45     9.15
- van de Boer SuperDash     8.90 0.178 81     8.55     9.26
-
-Confidence level used: 0.95 

results/raw/fertilzer_trial_stats.txt

@@ -7,7 +7,7 @@ farm        2   0.279   0.139   0.2634 0.7691
 fertilizer  2 259.292 129.646 245.1385 <2e-16 ***
 Residuals  81  42.838   0.529                    
 ---
-Signif. codes:  0 *** 0.001 ** 0.01 * 0.05 . 0.1   1
+Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
 [1] "em means table:"
  farm        fertilizer  emmean    SE df lower.CL upper.CL
  de Jong     Efficientie  12.93 0.173 81    12.59    13.28

scripts/2_data_cleaning.R

@@ -58,7 +58,7 @@ lapply(sheet_names, function(x) addWorksheet(wb, sheetName = x))
 mapply(function(name, data) writeData(wb, name, data), sheet_names, sheet_data)
 
 saveWorkbook(wb = wb,
-             file = "./data/processed/fertilizer_trial_WUR_cleaned.xlsx",
+             file = "./data/cleaned/fertilizer_trial_WUR_cleaned.xlsx",
              overwrite = TRUE)
 
 

scripts/3_analysis.R

@@ -8,7 +8,7 @@ library(emmeans)
 
 ##### Load data ------------------------------------------------------------------------------------
 
-d <- read.xlsx("./data/processed/fertilizer_trial_WUR_cleaned.xlsx",
+d <- read.xlsx("./data/cleaned/fertilizer_trial_WUR_cleaned.xlsx",
                 sheet = "data")
 
 ##### Analysis -------------------------------------------------------------------------------------
@@ -26,7 +26,7 @@ summary_plot <- ggplot(d) + # initialize graph
 summary_plot
 
 # Save the summary plot
-ggsave(filename = "./results/figures/2.summary_plot.png",
+ggsave(filename = "./results/figures/summary_plot.png",
        plot = summary_plot)
 
 
@@ -71,5 +71,5 @@ emms_plot <- ggplot(d) +
 emms_plot
 
 # Save the fancy plot
-ggsave(filename = "./results/figures/2.emms_plot.png",
+ggsave(filename = "./results/figures/emms_plot.png",
        plot = emms_plot)